Hmdb loader

Showing metabocard for all-trans-Decaprenyl diphosphate (HMDB0059616)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (2) Show 2 proteinsXML
enzymes (2) Show 2 proteins
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-10-30 10:32:48 UTC
Update Date2022-03-07 03:17:34 UTC
HMDB IDHMDB0059616
Secondary Accession Numbers
  • HMDB59616
Metabolite Identification
Common Nameall-trans-Decaprenyl diphosphate
Descriptionall-trans-Decaprenyl diphosphate belongs to the class of organic compounds known as bactoprenol diphosphates. These are polyprenyl compounds consisting of a diphosphate group substituted by a bactoprenyl moiety. all-trans-Decaprenyl diphosphate is a moderately acidic compound (based on its pKa).
Structure
Data?1563865955
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0059616 (all-trans-Decaprenyl diphosphate)

Structure #1
  Mrv0541 02241207102D          

 59 58  0  0  0  0            999 V2000
  -22.6875  -13.5749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -22.6875  -12.1460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -20.2125  -10.7171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.7375   -9.2881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.2625   -7.8592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.7875   -6.4302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3125   -5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8375   -3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3625   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -21.0375  -12.1460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -18.5625  -10.7171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.0875   -9.2881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.6125   -7.8592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1375   -6.4302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6625   -5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1875   -3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7125   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -21.4500  -12.8605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -20.2125  -12.1460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -18.9750  -11.4315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.7375  -10.7171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.5000  -10.0026    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.2625   -9.2881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.0250   -8.5737    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.7875   -7.8592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.5500   -7.1447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3125   -6.4302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0750   -5.7158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8375   -5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6000   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3625   -3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1250   -2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -22.2750  -12.8605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -19.8000  -11.4315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.3250  -10.0026    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.8500   -8.5737    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3750   -7.1447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9000   -5.7158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4250   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9500   -2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    4.2868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    3.9849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    3.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    3.5724    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  1 41  1  0  0  0  0
  2 41  1  0  0  0  0
  3 42  1  0  0  0  0
  4 43  1  0  0  0  0
  5 44  1  0  0  0  0
  6 45  1  0  0  0  0
  7 46  1  0  0  0  0
  8 47  1  0  0  0  0
  9 48  1  0  0  0  0
 10 49  1  0  0  0  0
 11 50  1  0  0  0  0
 12 21  1  0  0  0  0
 12 22  1  0  0  0  0
 23 13  1  4  0  0  0
 13 24  1  0  0  0  0
 25 14  1  4  0  0  0
 14 26  1  0  0  0  0
 27 15  1  4  0  0  0
 15 28  1  0  0  0  0
 29 16  1  4  0  0  0
 16 30  1  0  0  0  0
 31 17  1  4  0  0  0
 17 32  1  0  0  0  0
 33 18  1  4  0  0  0
 18 34  1  0  0  0  0
 35 19  1  4  0  0  0
 19 36  1  0  0  0  0
 37 20  1  4  0  0  0
 20 38  1  0  0  0  0
 21 41  2  0  0  0  0
 22 42  1  0  0  0  0
 23 42  2  0  0  0  0
 24 43  1  0  0  0  0
 25 43  2  0  0  0  0
 26 44  1  0  0  0  0
 27 44  2  0  0  0  0
 28 45  1  0  0  0  0
 29 45  2  0  0  0  0
 30 46  1  0  0  0  0
 31 46  2  0  0  0  0
 32 47  1  0  0  0  0
 33 47  2  0  0  0  0
 34 48  1  0  0  0  0
 35 48  2  0  0  0  0
 36 49  1  0  0  0  0
 37 49  2  0  0  0  0
 38 50  1  0  0  0  0
 39 40  1  4  0  0  0
 39 50  2  0  0  0  0
 40 56  1  0  0  0  0
 51 58  1  0  0  0  0
 52 58  1  0  0  0  0
 53 58  2  0  0  0  0
 54 59  1  0  0  0  0
 55 59  2  0  0  0  0
 56 59  1  0  0  0  0
 57 58  1  0  0  0  0
 57 59  1  0  0  0  0
M  END
Download

3D MOL for HMDB0059616 (all-trans-Decaprenyl diphosphate)

HMDB0059616
     RDKit          3D
all-trans-Decaprenyl diphosphate
143142  0  0  0  0  0  0  0  0999 V2000
  -16.9230    1.9513   -1.3800 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.2282    0.5890   -1.8987 C   0  0  0  0  0  0  0  0  0  0  0  0
  -18.3264   -0.1883   -1.2112 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.5940    0.0405   -2.9113 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.5129    0.7159   -3.6396 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.1951   -0.0015   -3.5795 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.6482   -0.1665   -2.2161 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.3830   -0.9371   -1.1821 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.4560    0.4047   -1.9688 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.8394    0.2915   -0.6389 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4453   -0.3776   -0.6855 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9847   -0.4151    0.6997 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.8452   -1.2026    1.6709 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9095    0.1645    1.1508 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9852    0.9522    0.3089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5824    0.3805    0.6332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6122    1.1616   -0.1575 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6212    2.6624    0.0755 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7923    0.6279   -1.0027 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6603   -0.7892   -1.3319 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2279   -1.1976   -0.9145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1631   -0.9535    0.5585 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0753   -1.7898    1.4233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3587   -0.1119    1.1498 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3488    0.7675    0.5390 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0727    0.6852    1.3053 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6027   -0.5964    1.4014 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1271   -1.7504    2.0462 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8156   -0.8130    0.9833 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6889    0.1500    0.3624 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1929   -0.2230   -0.9841 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9930   -1.4455   -1.0148 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2954   -2.7780   -0.8300 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2877   -1.4251   -1.2735 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0610   -0.2189   -1.5466 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0846    0.7563   -0.4426 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6707    0.3085    0.8676 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4901    1.3180    1.9714 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2344   -0.8338    1.0675 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8622   -1.5115    2.1856 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0990   -0.8568    3.4737 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0223    0.2802    3.5127 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1830    1.0351    4.7975 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7268    0.6915    2.4753 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6287    1.8419    2.5892 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0591    1.4487    2.5364 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5453    0.7544    1.3447 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0552   -0.6064    0.9631 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4873    1.3550    0.6198 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0029    0.6734   -0.5990 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3823    0.5007   -0.3690 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0434   -0.2709   -1.7091 P   0  0  0  0  0  5  0  0  0  0  0  0
   15.2913   -1.5553   -2.0531 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.6845   -0.5936   -1.4329 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9662    0.7777   -3.0303 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.2013    0.3330   -4.1086 P   0  0  0  0  0  5  0  0  0  0  0  0
   16.8537   -1.0151   -4.7185 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.6308    0.1889   -3.2235 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.3102    1.4998   -5.3135 O   0  0  0  0  0  0  0  0  0  0  0  0
  -17.3580    2.0697   -0.3830 H   0  0  0  0  0  0  0  0  0  0  0  0
  -17.3512    2.7482   -2.0202 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.8164    2.0637   -1.2806 H   0  0  0  0  0  0  0  0  0  0  0  0
  -19.3163    0.1136   -1.6122 H   0  0  0  0  0  0  0  0  0  0  0  0
  -18.3142    0.0098   -0.1252 H   0  0  0  0  0  0  0  0  0  0  0  0
  -18.1292   -1.2890   -1.3376 H   0  0  0  0  0  0  0  0  0  0  0  0
  -16.8850   -0.9684   -3.2388 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.7771    0.7834   -4.7289 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.3852    1.7627   -3.2474 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.4781    0.5054   -4.2527 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.3504   -1.0175   -4.0055 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.6557   -1.6306   -0.7028 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.8357   -0.2469   -0.4470 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.1762   -1.5313   -1.6953 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.9371    0.9558   -2.7534 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6516    1.3138   -0.2263 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.4251   -0.2739    0.0968 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5942   -1.3933   -1.1164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8497    0.1860   -1.3964 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6558   -0.5326    1.9800 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2538   -1.4992    2.5570 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1849   -2.1120    1.1331 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6379    0.0814    2.2302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9849    2.0338    0.5603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1428    0.7761   -0.7505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4366    0.5928    1.7284 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5935   -0.6835    0.4396 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6568    3.0934   -0.1765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8877    2.8314    1.1352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4123    3.1164   -0.5337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1080    1.3114   -1.5460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7648   -0.9860   -2.4384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3379   -1.4853   -0.8454 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0973   -2.2747   -1.0812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4697   -0.6518   -1.4843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3848   -2.4519    2.0094 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6473   -2.4682    0.7745 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6828   -1.1629    2.0706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4516   -0.0373    2.2595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6804    1.8381    0.5941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1829    0.5655   -0.5376 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6444    1.5039    1.0020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3451    1.0497    2.3756 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6641   -2.4917    2.3429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6593   -1.3689    2.9324 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7847   -2.2826    1.3676 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2043   -1.8398    1.1713 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3147    1.1953    0.2736 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5648    0.2912    1.0878 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2595   -0.4943   -1.6496 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6382    0.5934   -1.5745 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2047   -2.6876   -0.9057 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6670   -3.4744   -1.6512 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6146   -3.2749    0.0943 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7937   -2.4090   -1.3001 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6216    0.3086   -2.4419 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1185   -0.5302   -1.8039 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1976    1.3649   -0.2607 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8575    1.5873   -0.7433 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3326    2.0235    1.9573 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5923    1.9717    1.7253 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2575    0.8505    2.9177 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2689   -1.4515    0.0934 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2909   -2.4837    2.4339 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8690   -1.9123    1.8201 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1832   -0.7184    4.1124 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6080   -1.7173    4.1110 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7986    2.0674    4.7235 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6196    0.5166    5.5860 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2473    1.0351    5.1097 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6117    0.1785    1.5372 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.3890    2.6249    1.8024 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.4378    2.4075    3.5530 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.6489    2.4065    2.6797 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.2470    0.7866    3.4370 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3543   -0.5951    0.1153 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.9359   -1.2983    0.7875 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.5445   -1.0669    1.8393 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.8630    2.3266    0.9269 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.9434    1.4059   -1.4390 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.4773   -0.2577   -0.8131 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.0562   -0.0642   -0.6855 H   0  0  0  0  0  0  0  0  0  0  0  0
   19.0528   -0.6995   -3.4087 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.2007    1.0732   -6.1905 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  3
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  2  3
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 17 19  2  3
 19 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  1  0
 22 24  2  3
 24 25  1  0
 25 26  1  0
 26 27  1  0
 27 28  1  0
 27 29  2  3
 29 30  1  0
 30 31  1  0
 31 32  1  0
 32 33  1  0
 32 34  2  3
 34 35  1  0
 35 36  1  0
 36 37  1  0
 37 38  1  0
 37 39  2  3
 39 40  1  0
 40 41  1  0
 41 42  1  0
 42 43  1  0
 42 44  2  3
 44 45  1  0
 45 46  1  0
 46 47  1  0
 47 48  1  0
 47 49  2  3
 49 50  1  0
 50 51  1  0
 51 52  1  0
 52 53  2  0
 52 54  1  0
 52 55  1  0
 55 56  1  0
 56 57  2  0
 56 58  1  0
 56 59  1  0
  1 60  1  0
  1 61  1  0
  1 62  1  0
  3 63  1  0
  3 64  1  0
  3 65  1  0
  4 66  1  0
  5 67  1  0
  5 68  1  0
  6 69  1  0
  6 70  1  0
  8 71  1  0
  8 72  1  0
  8 73  1  0
  9 74  1  0
 10 75  1  0
 10 76  1  0
 11 77  1  0
 11 78  1  0
 13 79  1  0
 13 80  1  0
 13 81  1  0
 14 82  1  0
 15 83  1  0
 15 84  1  0
 16 85  1  0
 16 86  1  0
 18 87  1  0
 18 88  1  0
 18 89  1  0
 19 90  1  0
 20 91  1  0
 20 92  1  0
 21 93  1  0
 21 94  1  0
 23 95  1  0
 23 96  1  0
 23 97  1  0
 24 98  1  0
 25 99  1  0
 25100  1  0
 26101  1  0
 26102  1  0
 28103  1  0
 28104  1  0
 28105  1  0
 29106  1  0
 30107  1  0
 30108  1  0
 31109  1  0
 31110  1  0
 33111  1  0
 33112  1  0
 33113  1  0
 34114  1  0
 35115  1  0
 35116  1  0
 36117  1  0
 36118  1  0
 38119  1  0
 38120  1  0
 38121  1  0
 39122  1  0
 40123  1  0
 40124  1  0
 41125  1  0
 41126  1  0
 43127  1  0
 43128  1  0
 43129  1  0
 44130  1  0
 45131  1  0
 45132  1  0
 46133  1  0
 46134  1  0
 48135  1  0
 48136  1  0
 48137  1  0
 49138  1  0
 50139  1  0
 50140  1  0
 54141  1  0
 58142  1  0
 59143  1  0
M  END
Download

3D SDF for HMDB0059616 (all-trans-Decaprenyl diphosphate)

Structure #1
  Mrv0541 02241207102D          

 59 58  0  0  0  0            999 V2000
  -22.6875  -13.5749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -22.6875  -12.1460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -20.2125  -10.7171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.7375   -9.2881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.2625   -7.8592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.7875   -6.4302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3125   -5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8375   -3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3625   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -21.0375  -12.1460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -18.5625  -10.7171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.0875   -9.2881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.6125   -7.8592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1375   -6.4302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6625   -5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1875   -3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7125   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -21.4500  -12.8605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -20.2125  -12.1460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -18.9750  -11.4315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.7375  -10.7171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.5000  -10.0026    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.2625   -9.2881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.0250   -8.5737    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.7875   -7.8592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.5500   -7.1447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3125   -6.4302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0750   -5.7158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8375   -5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6000   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3625   -3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1250   -2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -22.2750  -12.8605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -19.8000  -11.4315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.3250  -10.0026    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.8500   -8.5737    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3750   -7.1447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9000   -5.7158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4250   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9500   -2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    4.2868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    3.9849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    3.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    3.5724    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  1 41  1  0  0  0  0
  2 41  1  0  0  0  0
  3 42  1  0  0  0  0
  4 43  1  0  0  0  0
  5 44  1  0  0  0  0
  6 45  1  0  0  0  0
  7 46  1  0  0  0  0
  8 47  1  0  0  0  0
  9 48  1  0  0  0  0
 10 49  1  0  0  0  0
 11 50  1  0  0  0  0
 12 21  1  0  0  0  0
 12 22  1  0  0  0  0
 23 13  1  4  0  0  0
 13 24  1  0  0  0  0
 25 14  1  4  0  0  0
 14 26  1  0  0  0  0
 27 15  1  4  0  0  0
 15 28  1  0  0  0  0
 29 16  1  4  0  0  0
 16 30  1  0  0  0  0
 31 17  1  4  0  0  0
 17 32  1  0  0  0  0
 33 18  1  4  0  0  0
 18 34  1  0  0  0  0
 35 19  1  4  0  0  0
 19 36  1  0  0  0  0
 37 20  1  4  0  0  0
 20 38  1  0  0  0  0
 21 41  2  0  0  0  0
 22 42  1  0  0  0  0
 23 42  2  0  0  0  0
 24 43  1  0  0  0  0
 25 43  2  0  0  0  0
 26 44  1  0  0  0  0
 27 44  2  0  0  0  0
 28 45  1  0  0  0  0
 29 45  2  0  0  0  0
 30 46  1  0  0  0  0
 31 46  2  0  0  0  0
 32 47  1  0  0  0  0
 33 47  2  0  0  0  0
 34 48  1  0  0  0  0
 35 48  2  0  0  0  0
 36 49  1  0  0  0  0
 37 49  2  0  0  0  0
 38 50  1  0  0  0  0
 39 40  1  4  0  0  0
 39 50  2  0  0  0  0
 40 56  1  0  0  0  0
 51 58  1  0  0  0  0
 52 58  1  0  0  0  0
 53 58  2  0  0  0  0
 54 59  1  0  0  0  0
 55 59  2  0  0  0  0
 56 59  1  0  0  0  0
 57 58  1  0  0  0  0
 57 59  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0059616

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCOP(O)(=O)OP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C50H84O7P2/c1-41(2)21-12-22-42(3)23-13-24-43(4)25-14-26-44(5)27-15-28-45(6)29-16-30-46(7)31-17-32-47(8)33-18-34-48(9)35-19-36-49(10)37-20-38-50(11)39-40-56-59(54,55)57-58(51,52)53/h21,23,25,27,29,31,33,35,37,39H,12-20,22,24,26,28,30,32,34,36,38,40H2,1-11H3,(H,54,55)(H2,51,52,53)

> <INCHI_KEY>
FSCYHDCTHRVSKN-UHFFFAOYSA-N

> <FORMULA>
C50H84O7P2

> <MOLECULAR_WEIGHT>
859.1453

> <EXACT_MASS>
858.569228066

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
103.91499821810635

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
({[(3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl)oxy](hydroxy)phosphoryl}oxy)phosphonic acid

> <ALOGPS_LOGP>
8.90

> <JCHEM_LOGP>
15.234732985666664

> <ALOGPS_LOGS>
-6.43

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.1843406094078315

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7672186885241006

> <JCHEM_POLAR_SURFACE_AREA>
113.29000000000002

> <JCHEM_REFRACTIVITY>
263.34870000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
32

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.23e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
decaprenyl diphosphate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0059616 (all-trans-Decaprenyl diphosphate)

HMDB0059616
     RDKit          3D
all-trans-Decaprenyl diphosphate
143142  0  0  0  0  0  0  0  0999 V2000
  -16.9230    1.9513   -1.3800 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.2282    0.5890   -1.8987 C   0  0  0  0  0  0  0  0  0  0  0  0
  -18.3264   -0.1883   -1.2112 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.5940    0.0405   -2.9113 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.5129    0.7159   -3.6396 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.1951   -0.0015   -3.5795 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.6482   -0.1665   -2.2161 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.3830   -0.9371   -1.1821 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.4560    0.4047   -1.9688 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.8394    0.2915   -0.6389 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4453   -0.3776   -0.6855 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9847   -0.4151    0.6997 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.8452   -1.2026    1.6709 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9095    0.1645    1.1508 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9852    0.9522    0.3089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5824    0.3805    0.6332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6122    1.1616   -0.1575 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6212    2.6624    0.0755 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7923    0.6279   -1.0027 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6603   -0.7892   -1.3319 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2279   -1.1976   -0.9145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1631   -0.9535    0.5585 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0753   -1.7898    1.4233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3587   -0.1119    1.1498 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3488    0.7675    0.5390 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0727    0.6852    1.3053 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6027   -0.5964    1.4014 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1271   -1.7504    2.0462 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8156   -0.8130    0.9833 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6889    0.1500    0.3624 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1929   -0.2230   -0.9841 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9930   -1.4455   -1.0148 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2954   -2.7780   -0.8300 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2877   -1.4251   -1.2735 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0610   -0.2189   -1.5466 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0846    0.7563   -0.4426 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6707    0.3085    0.8676 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4901    1.3180    1.9714 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2344   -0.8338    1.0675 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8622   -1.5115    2.1856 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0990   -0.8568    3.4737 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0223    0.2802    3.5127 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1830    1.0351    4.7975 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7268    0.6915    2.4753 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6287    1.8419    2.5892 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0591    1.4487    2.5364 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5453    0.7544    1.3447 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0552   -0.6064    0.9631 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4873    1.3550    0.6198 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0029    0.6734   -0.5990 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3823    0.5007   -0.3690 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0434   -0.2709   -1.7091 P   0  0  0  0  0  5  0  0  0  0  0  0
   15.2913   -1.5553   -2.0531 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.6845   -0.5936   -1.4329 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9662    0.7777   -3.0303 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.2013    0.3330   -4.1086 P   0  0  0  0  0  5  0  0  0  0  0  0
   16.8537   -1.0151   -4.7185 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.6308    0.1889   -3.2235 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.3102    1.4998   -5.3135 O   0  0  0  0  0  0  0  0  0  0  0  0
  -17.3580    2.0697   -0.3830 H   0  0  0  0  0  0  0  0  0  0  0  0
  -17.3512    2.7482   -2.0202 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.8164    2.0637   -1.2806 H   0  0  0  0  0  0  0  0  0  0  0  0
  -19.3163    0.1136   -1.6122 H   0  0  0  0  0  0  0  0  0  0  0  0
  -18.3142    0.0098   -0.1252 H   0  0  0  0  0  0  0  0  0  0  0  0
  -18.1292   -1.2890   -1.3376 H   0  0  0  0  0  0  0  0  0  0  0  0
  -16.8850   -0.9684   -3.2388 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.7771    0.7834   -4.7289 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.3852    1.7627   -3.2474 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.4781    0.5054   -4.2527 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.3504   -1.0175   -4.0055 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.6557   -1.6306   -0.7028 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.8357   -0.2469   -0.4470 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.1762   -1.5313   -1.6953 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.9371    0.9558   -2.7534 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6516    1.3138   -0.2263 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.4251   -0.2739    0.0968 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5942   -1.3933   -1.1164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8497    0.1860   -1.3964 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6558   -0.5326    1.9800 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2538   -1.4992    2.5570 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1849   -2.1120    1.1331 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6379    0.0814    2.2302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9849    2.0338    0.5603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1428    0.7761   -0.7505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4366    0.5928    1.7284 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5935   -0.6835    0.4396 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6568    3.0934   -0.1765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8877    2.8314    1.1352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4123    3.1164   -0.5337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1080    1.3114   -1.5460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7648   -0.9860   -2.4384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3379   -1.4853   -0.8454 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0973   -2.2747   -1.0812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4697   -0.6518   -1.4843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3848   -2.4519    2.0094 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6473   -2.4682    0.7745 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6828   -1.1629    2.0706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4516   -0.0373    2.2595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6804    1.8381    0.5941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1829    0.5655   -0.5376 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6444    1.5039    1.0020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3451    1.0497    2.3756 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6641   -2.4917    2.3429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6593   -1.3689    2.9324 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7847   -2.2826    1.3676 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2043   -1.8398    1.1713 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3147    1.1953    0.2736 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5648    0.2912    1.0878 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2595   -0.4943   -1.6496 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6382    0.5934   -1.5745 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2047   -2.6876   -0.9057 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6670   -3.4744   -1.6512 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6146   -3.2749    0.0943 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7937   -2.4090   -1.3001 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6216    0.3086   -2.4419 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1185   -0.5302   -1.8039 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1976    1.3649   -0.2607 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8575    1.5873   -0.7433 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3326    2.0235    1.9573 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5923    1.9717    1.7253 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2575    0.8505    2.9177 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2689   -1.4515    0.0934 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2909   -2.4837    2.4339 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8690   -1.9123    1.8201 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1832   -0.7184    4.1124 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6080   -1.7173    4.1110 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7986    2.0674    4.7235 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6196    0.5166    5.5860 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2473    1.0351    5.1097 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6117    0.1785    1.5372 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.3890    2.6249    1.8024 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.4378    2.4075    3.5530 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.6489    2.4065    2.6797 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.2470    0.7866    3.4370 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3543   -0.5951    0.1153 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.9359   -1.2983    0.7875 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.5445   -1.0669    1.8393 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.8630    2.3266    0.9269 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.9434    1.4059   -1.4390 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.4773   -0.2577   -0.8131 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.0562   -0.0642   -0.6855 H   0  0  0  0  0  0  0  0  0  0  0  0
   19.0528   -0.6995   -3.4087 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.2007    1.0732   -6.1905 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  3
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  2  3
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 17 19  2  3
 19 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  1  0
 22 24  2  3
 24 25  1  0
 25 26  1  0
 26 27  1  0
 27 28  1  0
 27 29  2  3
 29 30  1  0
 30 31  1  0
 31 32  1  0
 32 33  1  0
 32 34  2  3
 34 35  1  0
 35 36  1  0
 36 37  1  0
 37 38  1  0
 37 39  2  3
 39 40  1  0
 40 41  1  0
 41 42  1  0
 42 43  1  0
 42 44  2  3
 44 45  1  0
 45 46  1  0
 46 47  1  0
 47 48  1  0
 47 49  2  3
 49 50  1  0
 50 51  1  0
 51 52  1  0
 52 53  2  0
 52 54  1  0
 52 55  1  0
 55 56  1  0
 56 57  2  0
 56 58  1  0
 56 59  1  0
  1 60  1  0
  1 61  1  0
  1 62  1  0
  3 63  1  0
  3 64  1  0
  3 65  1  0
  4 66  1  0
  5 67  1  0
  5 68  1  0
  6 69  1  0
  6 70  1  0
  8 71  1  0
  8 72  1  0
  8 73  1  0
  9 74  1  0
 10 75  1  0
 10 76  1  0
 11 77  1  0
 11 78  1  0
 13 79  1  0
 13 80  1  0
 13 81  1  0
 14 82  1  0
 15 83  1  0
 15 84  1  0
 16 85  1  0
 16 86  1  0
 18 87  1  0
 18 88  1  0
 18 89  1  0
 19 90  1  0
 20 91  1  0
 20 92  1  0
 21 93  1  0
 21 94  1  0
 23 95  1  0
 23 96  1  0
 23 97  1  0
 24 98  1  0
 25 99  1  0
 25100  1  0
 26101  1  0
 26102  1  0
 28103  1  0
 28104  1  0
 28105  1  0
 29106  1  0
 30107  1  0
 30108  1  0
 31109  1  0
 31110  1  0
 33111  1  0
 33112  1  0
 33113  1  0
 34114  1  0
 35115  1  0
 35116  1  0
 36117  1  0
 36118  1  0
 38119  1  0
 38120  1  0
 38121  1  0
 39122  1  0
 40123  1  0
 40124  1  0
 41125  1  0
 41126  1  0
 43127  1  0
 43128  1  0
 43129  1  0
 44130  1  0
 45131  1  0
 45132  1  0
 46133  1  0
 46134  1  0
 48135  1  0
 48136  1  0
 48137  1  0
 49138  1  0
 50139  1  0
 50140  1  0
 54141  1  0
 58142  1  0
 59143  1  0
M  END
Download

PDB for HMDB0059616 (all-trans-Decaprenyl diphosphate)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0     -42.350 -25.340   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0     -42.350 -22.673   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0     -37.730 -20.005   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -33.110 -17.338   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0     -28.490 -14.671   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0     -23.870 -12.003   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0     -19.250  -9.336   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0     -14.630  -6.668   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0     -10.010  -4.001   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -5.390  -1.334   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0     -39.270 -22.673   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0     -34.650 -20.005   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0     -30.030 -17.338   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0     -25.410 -14.671   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0     -20.790 -12.003   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0     -16.170  -9.336   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0     -11.550  -6.668   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -6.930  -4.001   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -2.310  -1.334   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0     -40.040 -24.006   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0     -37.730 -22.673   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0     -35.420 -21.339   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0     -33.110 -20.005   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0     -30.800 -18.672   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0     -28.490 -17.338   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0     -26.180 -16.004   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0     -23.870 -14.671   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0     -21.560 -13.337   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0     -19.250 -12.003   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0     -16.940 -10.669   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0     -14.630  -9.336   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0     -12.320  -8.002   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0     -10.010  -6.668   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -7.700  -5.335   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -5.390  -4.001   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -3.080  -2.667   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0     -41.580 -24.006   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0     -36.960 -21.339   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0     -32.340 -18.672   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0     -27.720 -16.004   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0     -23.100 -13.337   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0     -18.480 -10.669   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0     -13.860  -8.002   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      -9.240  -5.335   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      -4.620  -2.667   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   51  O   UNK     0       1.540   8.002   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0       3.644   7.438   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0       0.976   5.898   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0       3.644   3.231   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0       0.976   4.771   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0       1.540   2.667   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0       3.080   5.335   0.000  0.00  0.00           O+0
HETATM   58  P   UNK     0       2.310   6.668   0.000  0.00  0.00           P+0
HETATM   59  P   UNK     0       2.310   4.001   0.000  0.00  0.00           P+0
CONECT    1   41                                                            
CONECT    2   41                                                            
CONECT    3   42                                                            
CONECT    4   43                                                            
CONECT    5   44                                                            
CONECT    6   45                                                            
CONECT    7   46                                                            
CONECT    8   47                                                            
CONECT    9   48                                                            
CONECT   10   49                                                            
CONECT   11   50                                                            
CONECT   12   21   22                                                       
CONECT   13   23   24                                                       
CONECT   14   25   26                                                       
CONECT   15   27   28                                                       
CONECT   16   29   30                                                       
CONECT   17   31   32                                                       
CONECT   18   33   34                                                       
CONECT   19   35   36                                                       
CONECT   20   37   38                                                       
CONECT   21   12   41                                                       
CONECT   22   12   42                                                       
CONECT   23   13   42                                                       
CONECT   24   13   43                                                       
CONECT   25   14   43                                                       
CONECT   26   14   44                                                       
CONECT   27   15   44                                                       
CONECT   28   15   45                                                       
CONECT   29   16   45                                                       
CONECT   30   16   46                                                       
CONECT   31   17   46                                                       
CONECT   32   17   47                                                       
CONECT   33   18   47                                                       
CONECT   34   18   48                                                       
CONECT   35   19   48                                                       
CONECT   36   19   49                                                       
CONECT   37   20   49                                                       
CONECT   38   20   50                                                       
CONECT   39   40   50                                                       
CONECT   40   39   56                                                       
CONECT   41    1    2   21                                                  
CONECT   42    3   22   23                                                  
CONECT   43    4   24   25                                                  
CONECT   44    5   26   27                                                  
CONECT   45    6   28   29                                                  
CONECT   46    7   30   31                                                  
CONECT   47    8   32   33                                                  
CONECT   48    9   34   35                                                  
CONECT   49   10   36   37                                                  
CONECT   50   11   38   39                                                  
CONECT   51   58                                                            
CONECT   52   58                                                            
CONECT   53   58                                                            
CONECT   54   59                                                            
CONECT   55   59                                                            
CONECT   56   40   59                                                       
CONECT   57   58   59                                                       
CONECT   58   51   52   53   57                                             
CONECT   59   54   55   56   57                                             
MASTER        0    0    0    0    0    0    0    0   59    0  116    0
END
Download

3D PDB for HMDB0059616 (all-trans-Decaprenyl diphosphate)

COMPND    HMDB0059616
HETATM    1  C1  UNL     1     -16.923   1.951  -1.380  1.00  0.00           C  
HETATM    2  C2  UNL     1     -17.228   0.589  -1.899  1.00  0.00           C  
HETATM    3  C3  UNL     1     -18.326  -0.188  -1.211  1.00  0.00           C  
HETATM    4  C4  UNL     1     -16.594   0.041  -2.911  1.00  0.00           C  
HETATM    5  C5  UNL     1     -15.513   0.716  -3.640  1.00  0.00           C  
HETATM    6  C6  UNL     1     -14.195  -0.001  -3.580  1.00  0.00           C  
HETATM    7  C7  UNL     1     -13.648  -0.166  -2.216  1.00  0.00           C  
HETATM    8  C8  UNL     1     -14.383  -0.937  -1.182  1.00  0.00           C  
HETATM    9  C9  UNL     1     -12.456   0.405  -1.969  1.00  0.00           C  
HETATM   10  C10 UNL     1     -11.839   0.291  -0.639  1.00  0.00           C  
HETATM   11  C11 UNL     1     -10.445  -0.378  -0.686  1.00  0.00           C  
HETATM   12  C12 UNL     1      -9.985  -0.415   0.700  1.00  0.00           C  
HETATM   13  C13 UNL     1     -10.845  -1.203   1.671  1.00  0.00           C  
HETATM   14  C14 UNL     1      -8.910   0.164   1.151  1.00  0.00           C  
HETATM   15  C15 UNL     1      -7.985   0.952   0.309  1.00  0.00           C  
HETATM   16  C16 UNL     1      -6.582   0.381   0.633  1.00  0.00           C  
HETATM   17  C17 UNL     1      -5.612   1.162  -0.157  1.00  0.00           C  
HETATM   18  C18 UNL     1      -5.621   2.662   0.076  1.00  0.00           C  
HETATM   19  C19 UNL     1      -4.792   0.628  -1.003  1.00  0.00           C  
HETATM   20  C20 UNL     1      -4.660  -0.789  -1.332  1.00  0.00           C  
HETATM   21  C21 UNL     1      -3.228  -1.198  -0.915  1.00  0.00           C  
HETATM   22  C22 UNL     1      -3.163  -0.954   0.559  1.00  0.00           C  
HETATM   23  C23 UNL     1      -4.075  -1.790   1.423  1.00  0.00           C  
HETATM   24  C24 UNL     1      -2.359  -0.112   1.150  1.00  0.00           C  
HETATM   25  C25 UNL     1      -1.349   0.768   0.539  1.00  0.00           C  
HETATM   26  C26 UNL     1      -0.073   0.685   1.305  1.00  0.00           C  
HETATM   27  C27 UNL     1       0.603  -0.596   1.401  1.00  0.00           C  
HETATM   28  C28 UNL     1      -0.127  -1.750   2.046  1.00  0.00           C  
HETATM   29  C29 UNL     1       1.816  -0.813   0.983  1.00  0.00           C  
HETATM   30  C30 UNL     1       2.689   0.150   0.362  1.00  0.00           C  
HETATM   31  C31 UNL     1       3.193  -0.223  -0.984  1.00  0.00           C  
HETATM   32  C32 UNL     1       3.993  -1.445  -1.015  1.00  0.00           C  
HETATM   33  C33 UNL     1       3.295  -2.778  -0.830  1.00  0.00           C  
HETATM   34  C34 UNL     1       5.288  -1.425  -1.273  1.00  0.00           C  
HETATM   35  C35 UNL     1       6.061  -0.219  -1.547  1.00  0.00           C  
HETATM   36  C36 UNL     1       6.085   0.756  -0.443  1.00  0.00           C  
HETATM   37  C37 UNL     1       6.671   0.308   0.868  1.00  0.00           C  
HETATM   38  C38 UNL     1       6.490   1.318   1.971  1.00  0.00           C  
HETATM   39  C39 UNL     1       7.234  -0.834   1.067  1.00  0.00           C  
HETATM   40  C40 UNL     1       7.862  -1.512   2.186  1.00  0.00           C  
HETATM   41  C41 UNL     1       8.099  -0.857   3.474  1.00  0.00           C  
HETATM   42  C42 UNL     1       9.022   0.280   3.513  1.00  0.00           C  
HETATM   43  C43 UNL     1       9.183   1.035   4.798  1.00  0.00           C  
HETATM   44  C44 UNL     1       9.727   0.691   2.475  1.00  0.00           C  
HETATM   45  C45 UNL     1      10.629   1.842   2.589  1.00  0.00           C  
HETATM   46  C46 UNL     1      12.059   1.449   2.536  1.00  0.00           C  
HETATM   47  C47 UNL     1      12.545   0.754   1.345  1.00  0.00           C  
HETATM   48  C48 UNL     1      12.055  -0.606   0.963  1.00  0.00           C  
HETATM   49  C49 UNL     1      13.487   1.355   0.620  1.00  0.00           C  
HETATM   50  C50 UNL     1      14.003   0.673  -0.599  1.00  0.00           C  
HETATM   51  O1  UNL     1      15.382   0.501  -0.369  1.00  0.00           O  
HETATM   52  P1  UNL     1      16.043  -0.271  -1.709  1.00  0.00           P  
HETATM   53  O2  UNL     1      15.291  -1.555  -2.053  1.00  0.00           O  
HETATM   54  O3  UNL     1      17.684  -0.594  -1.433  1.00  0.00           O  
HETATM   55  O4  UNL     1      15.966   0.778  -3.030  1.00  0.00           O  
HETATM   56  P2  UNL     1      17.201   0.333  -4.109  1.00  0.00           P  
HETATM   57  O5  UNL     1      16.854  -1.015  -4.718  1.00  0.00           O  
HETATM   58  O6  UNL     1      18.631   0.189  -3.224  1.00  0.00           O  
HETATM   59  O7  UNL     1      17.310   1.500  -5.313  1.00  0.00           O  
HETATM   60  H1  UNL     1     -17.358   2.070  -0.383  1.00  0.00           H  
HETATM   61  H2  UNL     1     -17.351   2.748  -2.020  1.00  0.00           H  
HETATM   62  H3  UNL     1     -15.816   2.064  -1.281  1.00  0.00           H  
HETATM   63  H4  UNL     1     -19.316   0.114  -1.612  1.00  0.00           H  
HETATM   64  H5  UNL     1     -18.314   0.010  -0.125  1.00  0.00           H  
HETATM   65  H6  UNL     1     -18.129  -1.289  -1.338  1.00  0.00           H  
HETATM   66  H7  UNL     1     -16.885  -0.968  -3.239  1.00  0.00           H  
HETATM   67  H8  UNL     1     -15.777   0.783  -4.729  1.00  0.00           H  
HETATM   68  H9  UNL     1     -15.385   1.763  -3.247  1.00  0.00           H  
HETATM   69  H10 UNL     1     -13.478   0.505  -4.253  1.00  0.00           H  
HETATM   70  H11 UNL     1     -14.350  -1.018  -4.005  1.00  0.00           H  
HETATM   71  H12 UNL     1     -13.656  -1.631  -0.703  1.00  0.00           H  
HETATM   72  H13 UNL     1     -14.836  -0.247  -0.447  1.00  0.00           H  
HETATM   73  H14 UNL     1     -15.176  -1.531  -1.695  1.00  0.00           H  
HETATM   74  H15 UNL     1     -11.937   0.956  -2.753  1.00  0.00           H  
HETATM   75  H16 UNL     1     -11.652   1.314  -0.226  1.00  0.00           H  
HETATM   76  H17 UNL     1     -12.425  -0.274   0.097  1.00  0.00           H  
HETATM   77  H18 UNL     1     -10.594  -1.393  -1.116  1.00  0.00           H  
HETATM   78  H19 UNL     1      -9.850   0.186  -1.396  1.00  0.00           H  
HETATM   79  H20 UNL     1     -11.656  -0.533   1.980  1.00  0.00           H  
HETATM   80  H21 UNL     1     -10.254  -1.499   2.557  1.00  0.00           H  
HETATM   81  H22 UNL     1     -11.185  -2.112   1.133  1.00  0.00           H  
HETATM   82  H23 UNL     1      -8.638   0.081   2.230  1.00  0.00           H  
HETATM   83  H24 UNL     1      -7.985   2.034   0.560  1.00  0.00           H  
HETATM   84  H25 UNL     1      -8.143   0.776  -0.751  1.00  0.00           H  
HETATM   85  H26 UNL     1      -6.437   0.593   1.728  1.00  0.00           H  
HETATM   86  H27 UNL     1      -6.594  -0.683   0.440  1.00  0.00           H  
HETATM   87  H28 UNL     1      -4.657   3.093  -0.176  1.00  0.00           H  
HETATM   88  H29 UNL     1      -5.888   2.831   1.135  1.00  0.00           H  
HETATM   89  H30 UNL     1      -6.412   3.116  -0.534  1.00  0.00           H  
HETATM   90  H31 UNL     1      -4.108   1.311  -1.546  1.00  0.00           H  
HETATM   91  H32 UNL     1      -4.765  -0.986  -2.438  1.00  0.00           H  
HETATM   92  H33 UNL     1      -5.338  -1.485  -0.845  1.00  0.00           H  
HETATM   93  H34 UNL     1      -3.097  -2.275  -1.081  1.00  0.00           H  
HETATM   94  H35 UNL     1      -2.470  -0.652  -1.484  1.00  0.00           H  
HETATM   95  H36 UNL     1      -3.385  -2.452   2.009  1.00  0.00           H  
HETATM   96  H37 UNL     1      -4.647  -2.468   0.774  1.00  0.00           H  
HETATM   97  H38 UNL     1      -4.683  -1.163   2.071  1.00  0.00           H  
HETATM   98  H39 UNL     1      -2.452  -0.037   2.259  1.00  0.00           H  
HETATM   99  H40 UNL     1      -1.680   1.838   0.594  1.00  0.00           H  
HETATM  100  H41 UNL     1      -1.183   0.566  -0.538  1.00  0.00           H  
HETATM  101  H42 UNL     1       0.644   1.504   1.002  1.00  0.00           H  
HETATM  102  H43 UNL     1      -0.345   1.050   2.376  1.00  0.00           H  
HETATM  103  H44 UNL     1       0.664  -2.492   2.343  1.00  0.00           H  
HETATM  104  H45 UNL     1      -0.659  -1.369   2.932  1.00  0.00           H  
HETATM  105  H46 UNL     1      -0.785  -2.283   1.368  1.00  0.00           H  
HETATM  106  H47 UNL     1       2.204  -1.840   1.171  1.00  0.00           H  
HETATM  107  H48 UNL     1       2.315   1.195   0.274  1.00  0.00           H  
HETATM  108  H49 UNL     1       3.565   0.291   1.088  1.00  0.00           H  
HETATM  109  H50 UNL     1       2.260  -0.494  -1.650  1.00  0.00           H  
HETATM  110  H51 UNL     1       3.638   0.593  -1.575  1.00  0.00           H  
HETATM  111  H52 UNL     1       2.205  -2.688  -0.906  1.00  0.00           H  
HETATM  112  H53 UNL     1       3.667  -3.474  -1.651  1.00  0.00           H  
HETATM  113  H54 UNL     1       3.615  -3.275   0.094  1.00  0.00           H  
HETATM  114  H55 UNL     1       5.794  -2.409  -1.300  1.00  0.00           H  
HETATM  115  H56 UNL     1       5.622   0.309  -2.442  1.00  0.00           H  
HETATM  116  H57 UNL     1       7.119  -0.530  -1.804  1.00  0.00           H  
HETATM  117  H58 UNL     1       5.198   1.365  -0.261  1.00  0.00           H  
HETATM  118  H59 UNL     1       6.857   1.587  -0.743  1.00  0.00           H  
HETATM  119  H60 UNL     1       7.333   2.023   1.957  1.00  0.00           H  
HETATM  120  H61 UNL     1       5.592   1.972   1.725  1.00  0.00           H  
HETATM  121  H62 UNL     1       6.258   0.851   2.918  1.00  0.00           H  
HETATM  122  H63 UNL     1       7.269  -1.452   0.093  1.00  0.00           H  
HETATM  123  H64 UNL     1       7.291  -2.484   2.434  1.00  0.00           H  
HETATM  124  H65 UNL     1       8.869  -1.912   1.820  1.00  0.00           H  
HETATM  125  H66 UNL     1       7.183  -0.718   4.112  1.00  0.00           H  
HETATM  126  H67 UNL     1       8.608  -1.717   4.111  1.00  0.00           H  
HETATM  127  H68 UNL     1       8.799   2.067   4.723  1.00  0.00           H  
HETATM  128  H69 UNL     1       8.620   0.517   5.586  1.00  0.00           H  
HETATM  129  H70 UNL     1      10.247   1.035   5.110  1.00  0.00           H  
HETATM  130  H71 UNL     1       9.612   0.179   1.537  1.00  0.00           H  
HETATM  131  H72 UNL     1      10.389   2.625   1.802  1.00  0.00           H  
HETATM  132  H73 UNL     1      10.438   2.407   3.553  1.00  0.00           H  
HETATM  133  H74 UNL     1      12.649   2.407   2.680  1.00  0.00           H  
HETATM  134  H75 UNL     1      12.247   0.787   3.437  1.00  0.00           H  
HETATM  135  H76 UNL     1      11.354  -0.595   0.115  1.00  0.00           H  
HETATM  136  H77 UNL     1      12.936  -1.298   0.787  1.00  0.00           H  
HETATM  137  H78 UNL     1      11.544  -1.067   1.839  1.00  0.00           H  
HETATM  138  H79 UNL     1      13.863   2.327   0.927  1.00  0.00           H  
HETATM  139  H80 UNL     1      13.943   1.406  -1.439  1.00  0.00           H  
HETATM  140  H81 UNL     1      13.477  -0.258  -0.813  1.00  0.00           H  
HETATM  141  H82 UNL     1      18.056  -0.064  -0.686  1.00  0.00           H  
HETATM  142  H83 UNL     1      19.053  -0.700  -3.409  1.00  0.00           H  
HETATM  143  H84 UNL     1      17.201   1.073  -6.190  1.00  0.00           H  
CONECT    1    2   60   61   62
CONECT    2    3    4    4
CONECT    3   63   64   65
CONECT    4    5   66
CONECT    5    6   67   68
CONECT    6    7   69   70
CONECT    7    8    9    9
CONECT    8   71   72   73
CONECT    9   10   74
CONECT   10   11   75   76
CONECT   11   12   77   78
CONECT   12   13   14   14
CONECT   13   79   80   81
CONECT   14   15   82
CONECT   15   16   83   84
CONECT   16   17   85   86
CONECT   17   18   19   19
CONECT   18   87   88   89
CONECT   19   20   90
CONECT   20   21   91   92
CONECT   21   22   93   94
CONECT   22   23   24   24
CONECT   23   95   96   97
CONECT   24   25   98
CONECT   25   26   99  100
CONECT   26   27  101  102
CONECT   27   28   29   29
CONECT   28  103  104  105
CONECT   29   30  106
CONECT   30   31  107  108
CONECT   31   32  109  110
CONECT   32   33   34   34
CONECT   33  111  112  113
CONECT   34   35  114
CONECT   35   36  115  116
CONECT   36   37  117  118
CONECT   37   38   39   39
CONECT   38  119  120  121
CONECT   39   40  122
CONECT   40   41  123  124
CONECT   41   42  125  126
CONECT   42   43   44   44
CONECT   43  127  128  129
CONECT   44   45  130
CONECT   45   46  131  132
CONECT   46   47  133  134
CONECT   47   48   49   49
CONECT   48  135  136  137
CONECT   49   50  138
CONECT   50   51  139  140
CONECT   51   52
CONECT   52   53   53   54   55
CONECT   54  141
CONECT   55   56
CONECT   56   57   57   58   59
CONECT   58  142
CONECT   59  143
END
Download

SMILES for HMDB0059616 (all-trans-Decaprenyl diphosphate)

CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCOP(O)(=O)OP(O)(O)=O
Download

INCHI for HMDB0059616 (all-trans-Decaprenyl diphosphate)

InChI=1S/C50H84O7P2/c1-41(2)21-12-22-42(3)23-13-24-43(4)25-14-26-44(5)27-15-28-45(6)29-16-30-46(7)31-17-32-47(8)33-18-34-48(9)35-19-36-49(10)37-20-38-50(11)39-40-56-59(54,55)57-58(51,52)53/h21,23,25,27,29,31,33,35,37,39H,12-20,22,24,26,28,30,32,34,36,38,40H2,1-11H3,(H,54,55)(H2,51,52,53)
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
all-trans-Decaprenyl diphosphoric acidGenerator
Decaprenyl diphosphoric acidGenerator
Chemical FormulaC50H84O7P2
Average Molecular Weight859.1453
Monoisotopic Molecular Weight858.569228066
IUPAC Name({[(3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl)oxy](hydroxy)phosphoryl}oxy)phosphonic acid
Traditional Namedecaprenyl diphosphate
CAS Registry NumberNot Available
SMILES
CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCOP(O)(=O)OP(O)(O)=O
InChI Identifier
InChI=1S/C50H84O7P2/c1-41(2)21-12-22-42(3)23-13-24-43(4)25-14-26-44(5)27-15-28-45(6)29-16-30-46(7)31-17-32-47(8)33-18-34-48(9)35-19-36-49(10)37-20-38-50(11)39-40-56-59(54,55)57-58(51,52)53/h21,23,25,27,29,31,33,35,37,39H,12-20,22,24,26,28,30,32,34,36,38,40H2,1-11H3,(H,54,55)(H2,51,52,53)
InChI KeyFSCYHDCTHRVSKN-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as bactoprenol diphosphates. These are polyprenyl compounds consisting of a diphosphate group substituted by a bactoprenyl moiety.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassPolyprenols
Direct ParentBactoprenol diphosphates
Alternative Parents
Substituents
  • Polyterpenoid
  • Bactoprenol diphosphate
  • Polyprenyl diphosphate
  • Polyprenyl monophosphate
  • Organic pyrophosphate
  • Isoprenoid phosphate
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.00032 g/LALOGPS
logP8.9ALOGPS
logP15.23ChemAxon
logS-6.4ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area113.29 ŲChemAxon
Rotatable Bond Count32ChemAxon
Refractivity263.35 m³·mol⁻¹ChemAxon
Polarizability103.91 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+303.97131661259
DarkChem[M-H]-274.28631661259
DeepCCS[M+H]+270.09630932474
DeepCCS[M-H]-267.730932474
DeepCCS[M-2H]-300.58430932474
DeepCCS[M+Na]+275.94330932474
AllCCS[M+H]+291.432859911
AllCCS[M+H-H2O]+291.032859911
AllCCS[M+NH4]+291.832859911
AllCCS[M+Na]+291.932859911
AllCCS[M-H]-261.732859911
AllCCS[M+Na-2H]-265.332859911
AllCCS[M+HCOO]-269.332859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.5.8 minutes32390414
Predicted by Siyang on May 30, 202234.1615 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.06 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid6001.4 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid442.4 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid410.0 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid258.2 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid247.7 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1597.9 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid1674.5 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)135.1 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid3287.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid1422.8 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1199.9 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1333.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid616.5 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate241.9 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA887.8 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water11.3 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
all-trans-Decaprenyl diphosphateCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCOP(O)(=O)OP(O)(O)=O6084.8Standard polar33892256
all-trans-Decaprenyl diphosphateCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCOP(O)(=O)OP(O)(O)=O4700.6Standard non polar33892256
all-trans-Decaprenyl diphosphateCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCOP(O)(=O)OP(O)(O)=O5578.0Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-Decaprenyl diphosphate 10V, Positive-QTOFsplash10-0560-0200009460-3b1abcb01c8d9f4817fb2016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-Decaprenyl diphosphate 20V, Positive-QTOFsplash10-001i-1111109200-bceb19e3f40f2424887b2016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-Decaprenyl diphosphate 40V, Positive-QTOFsplash10-0f89-0232339000-5cde4543c96f6f88ff182016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-Decaprenyl diphosphate 10V, Negative-QTOFsplash10-0a4i-0400000090-d5f49448e5726abd3a0a2016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-Decaprenyl diphosphate 20V, Negative-QTOFsplash10-056r-7900000010-c51f65f9878cace4fa012016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-Decaprenyl diphosphate 40V, Negative-QTOFsplash10-004i-9000000000-0d9fac3c81a88e14dad12016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-Decaprenyl diphosphate 10V, Negative-QTOFsplash10-0a4i-0000000090-093ecf1c976d87a41f652021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-Decaprenyl diphosphate 20V, Negative-QTOFsplash10-0a4i-2400010290-bb5f10b91d3bd86a3e462021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-Decaprenyl diphosphate 40V, Negative-QTOFsplash10-056r-9400000000-c9258da5f7e1bcf309552021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-Decaprenyl diphosphate 10V, Positive-QTOFsplash10-0a4i-0100001490-59124ee62549de39e9ec2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-Decaprenyl diphosphate 20V, Positive-QTOFsplash10-00m0-0001007910-81a39312a6e8bb7dee6d2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-Decaprenyl diphosphate 40V, Positive-QTOFsplash10-00pi-0219555310-5c4773b5eb03f35064e42021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID4575322
KEGG Compound IDC17432
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5462210
PDB IDNot Available
ChEBI ID53043
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  3. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  4. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  5. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Enzymes

Enzyme Details
1. Decaprenyl-diphosphate synthase subunit 2
General function:
Not Available
Specific function:
Supplies decaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone-10.
Gene Name:
PDSS2
Uniprot ID:
Q86YH6
Molecular weight:
44128.17
Reactions
Farnesyl pyrophosphate + Isopentenyl pyrophosphate → Pyrophosphate + all-trans-Decaprenyl diphosphatedetails
Enzyme Details
2. Decaprenyl-diphosphate synthase subunit 1
General function:
Not Available
Specific function:
Supplies decaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone-10.
Gene Name:
PDSS1
Uniprot ID:
Q5T2R2
Molecular weight:
46260.6
Reactions
Farnesyl pyrophosphate + Isopentenyl pyrophosphate → Pyrophosphate + all-trans-Decaprenyl diphosphatedetails