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Showing metabocard for Dodecaprenyl diphosphate (HMDB0012217)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2009-04-06 16:21:11 UTC
Update Date2022-03-07 02:51:22 UTC
HMDB IDHMDB0012217
Secondary Accession Numbers
  • HMDB12217
Metabolite Identification
Common NameDodecaprenyl diphosphate
DescriptionDodecaprenyl diphosphate is a polyisoprenoid, which contains multiple isoprene units. It is an intermediate in tridecaprenyl diphosphate, menaquinone-12 (vitamin K2)and linoleate biosynthesis. Dodecaprenyl diphosphate is converted. from undecaprenyl diphosphate and is converted to tridecaprenyl diphosphate via the enzyme solanesyl-diphosphate synthase (EC 2.5.1.11).
Structure
Data?1582753028
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0012217 (Dodecaprenyl diphosphate)


  Mrv0541 02241203502D          

 69 68  0  0  0  0            999 V2000
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M  END
Download

3D MOL for HMDB0012217 (Dodecaprenyl diphosphate)

HMDB0012217
     RDKit          3D
Dodecaprenyl diphosphate
169168  0  0  0  0  0  0  0  0999 V2000
  -19.7957    2.3044   -1.4344 C   0  0  0  0  0  0  0  0  0  0  0  0
  -19.9262    0.8615   -1.6871 C   0  0  0  0  0  0  0  0  0  0  0  0
  -20.4856    0.4183   -3.0057 C   0  0  0  0  0  0  0  0  0  0  0  0
  -19.5633   -0.0299   -0.7815 C   0  0  0  0  0  0  0  0  0  0  0  0
  -19.0057    0.3803    0.5368 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.6224   -0.1835    0.6890 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.0167    0.1752    2.0283 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.8407    1.6051    2.3551 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.6704   -0.8106    2.8594 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.0734   -0.4981    4.1730 C   0  0  0  0  0  0  0  0  0  0  0  0
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  -10.2185    0.3522   -2.1352 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1801   -0.5965   -2.6133 C   0  0  0  0  0  0  0  0  0  0  0  0
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   18.0154    0.3026   -1.1340 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5056    1.6851   -1.0326 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9090   -0.1559   -0.2837 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.4217    0.5773    0.8797 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9055    1.8390    1.0736 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.5955    2.5494    2.4618 P   0  0  0  0  0  5  0  0  0  0  0  0
   19.8607    4.0210    2.2092 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.0601    1.8008    2.8141 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.5274    2.4546    3.7703 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.5900    0.9717    4.5549 P   0  0  0  0  0  5  0  0  0  0  0  0
   17.5503    0.0526    3.9685 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.2483    1.1209    6.2164 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.1173    0.2425    4.3678 O   0  0  0  0  0  0  0  0  0  0  0  0
  -18.7378    2.6490   -1.3666 H   0  0  0  0  0  0  0  0  0  0  0  0
  -20.2651    2.9096   -2.2472 H   0  0  0  0  0  0  0  0  0  0  0  0
  -20.2907    2.6296   -0.4990 H   0  0  0  0  0  0  0  0  0  0  0  0
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  -17.2159    1.8505    3.3734 H   0  0  0  0  0  0  0  0  0  0  0  0
  -17.4778    2.2055    1.6682 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.7862    1.9586    2.2972 H   0  0  0  0  0  0  0  0  0  0  0  0
  -16.8520   -1.8299    2.5145 H   0  0  0  0  0  0  0  0  0  0  0  0
  -16.7591   -0.8631    4.9680 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.8917    0.5851    4.2335 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.9161   -2.2661    4.3145 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0012217 (Dodecaprenyl diphosphate)


  Mrv0541 02241203502D          

 69 68  0  0  0  0            999 V2000
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 19 17  1  0  0  0  0
 20 18  1  0  0  0  0
 21 20  1  0  0  0  0
 22 21  1  0  0  0  0
 23 22  2  0  0  0  0
 24 22  1  0  0  0  0
 25 23  1  0  0  0  0
 26 25  1  0  0  0  0
 27 26  1  0  0  0  0
 28 27  2  0  0  0  0
 29 27  1  0  0  0  0
 30 28  1  0  0  0  0
 31 30  1  0  0  0  0
 32 31  1  0  0  0  0
 33 32  2  0  0  0  0
 34 32  1  0  0  0  0
 35 33  1  0  0  0  0
 36 35  1  0  0  0  0
 37 36  1  0  0  0  0
 38 37  2  0  0  0  0
 39 37  1  0  0  0  0
 40 38  1  0  0  0  0
 41 40  1  0  0  0  0
 42 41  1  0  0  0  0
 43 42  2  0  0  0  0
 44 42  1  0  0  0  0
 45 43  1  0  0  0  0
 46 45  1  0  0  0  0
 47 46  1  0  0  0  0
 48 47  2  0  0  0  0
 49 47  1  0  0  0  0
 50 48  1  0  0  0  0
 51 50  1  0  0  0  0
 52 51  1  0  0  0  0
 53 52  2  0  0  0  0
 54 52  1  0  0  0  0
 55 53  1  0  0  0  0
 56 55  1  0  0  0  0
 57 56  1  0  0  0  0
 58 57  2  0  0  0  0
 59 57  1  0  0  0  0
 60 58  1  0  0  0  0
 61 60  1  0  0  0  0
 63 62  2  0  0  0  0
 64 62  1  0  0  0  0
 65 62  1  0  0  0  0
 61 62  1  0  0  0  0
 67 66  2  0  0  0  0
 68 66  1  0  0  0  0
 69 66  1  0  0  0  0
 64 66  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0012217

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)=CCC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\COP(O)(=O)OP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C60H100O7P2/c1-49(2)25-14-26-50(3)27-15-28-51(4)29-16-30-52(5)31-17-32-53(6)33-18-34-54(7)35-19-36-55(8)37-20-38-56(9)39-21-40-57(10)41-22-42-58(11)43-23-44-59(12)45-24-46-60(13)47-48-66-69(64,65)67-68(61,62)63/h25,27,29,31,33,35,37,39,41,43,45,47H,14-24,26,28,30,32,34,36,38,40,42,44,46,48H2,1-13H3,(H,64,65)(H2,61,62,63)/b50-27+,51-29+,52-31+,53-33+,54-35+,55-37+,56-39+,57-41+,58-43+,59-45+,60-47+

> <INCHI_KEY>
WURMRKUXTPWSRM-GNZYJLLNSA-N

> <FORMULA>
C60H100O7P2

> <MOLECULAR_WEIGHT>
995.3793

> <EXACT_MASS>
994.694428578

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
124.60047585967473

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[({[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E,42E)-3,7,11,15,19,23,27,31,35,39,43,47-dodecamethyloctatetraconta-2,6,10,14,18,22,26,30,34,38,42,46-dodecaen-1-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonic acid

> <ALOGPS_LOGP>
9.58

> <JCHEM_LOGP>
18.554161535666665

> <ALOGPS_LOGS>
-6.42

> <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>
310.9538999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
38

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.83e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E,42E)-3,7,11,15,19,23,27,31,35,39,43,47-dodecamethyloctatetraconta-2,6,10,14,18,22,26,30,34,38,42,46-dodecaen-1-yl]oxy(hydroxy)phosphoryl}oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0012217 (Dodecaprenyl diphosphate)

HMDB0012217
     RDKit          3D
Dodecaprenyl diphosphate
169168  0  0  0  0  0  0  0  0999 V2000
  -19.7957    2.3044   -1.4344 C   0  0  0  0  0  0  0  0  0  0  0  0
  -19.9262    0.8615   -1.6871 C   0  0  0  0  0  0  0  0  0  0  0  0
  -20.4856    0.4183   -3.0057 C   0  0  0  0  0  0  0  0  0  0  0  0
  -19.5633   -0.0299   -0.7815 C   0  0  0  0  0  0  0  0  0  0  0  0
  -19.0057    0.3803    0.5368 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.6224   -0.1835    0.6890 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.0167    0.1752    2.0283 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.8407    1.6051    2.3551 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.6704   -0.8106    2.8594 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.0734   -0.4981    4.1730 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.7362   -1.1939    4.3444 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.8062   -0.7120    3.3044 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.3828    0.7197    3.2612 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.2836   -1.4927    2.3731 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3516   -0.9517    1.3555 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.0615   -1.0124    0.0261 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.2548   -0.5321   -1.1008 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.8476   -0.4960   -2.4602 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.9586   -0.1206   -0.9530 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2185    0.3522   -2.1352 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1801   -0.5965   -2.6133 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0855   -0.8413   -1.6921 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0522   -1.8891   -2.0867 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8778   -0.2282   -0.5171 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7122   -0.6161    0.2941 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6974    0.4821    0.4250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5333   -0.0771    1.2078 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7285   -0.5502    2.5903 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3701   -0.1152    0.6041 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1635   -0.6421    1.2522 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0220    0.3269    1.2656 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1605   -0.3934    1.8822 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1171   -0.8852    3.2650 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2442   -0.5743    1.1496 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4476   -1.2549    1.6114 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7295   -0.5144    1.5951 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1478    0.0482    0.3011 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4021    1.1823   -0.2896 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2311   -0.3805   -0.3835 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6360    0.2012   -1.6826 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0911    0.5301   -1.7947 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8813   -0.7242   -1.6737 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6820   -1.8023   -2.6533 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7517   -0.8669   -0.7113 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6090   -2.0509   -0.4623 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0542   -1.6133   -0.4909 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3194   -1.0163   -1.8535 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1791   -1.7819   -3.0965 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7083    0.2484   -1.9270 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0126    1.0095   -3.1402 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4363    1.5349   -3.1652 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3682    0.3795   -3.1635 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3447   -0.5747   -4.3004 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2538    0.1770   -2.1701 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1732   -0.9508   -2.1592 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.6022   -0.5751   -2.2548 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.0154    0.3026   -1.1340 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5056    1.6851   -1.0326 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9090   -0.1559   -0.2837 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.4217    0.5773    0.8797 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9055    1.8390    1.0736 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.5955    2.5494    2.4618 P   0  0  0  0  0  5  0  0  0  0  0  0
   19.8607    4.0210    2.2092 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.0601    1.8008    2.8141 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.5274    2.4546    3.7703 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.5900    0.9717    4.5549 P   0  0  0  0  0  5  0  0  0  0  0  0
   17.5503    0.0526    3.9685 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.2483    1.1209    6.2164 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.1173    0.2425    4.3678 O   0  0  0  0  0  0  0  0  0  0  0  0
  -18.7378    2.6490   -1.3666 H   0  0  0  0  0  0  0  0  0  0  0  0
  -20.2651    2.9096   -2.2472 H   0  0  0  0  0  0  0  0  0  0  0  0
  -20.2907    2.6296   -0.4990 H   0  0  0  0  0  0  0  0  0  0  0  0
  -21.0186    1.2396   -3.5259 H   0  0  0  0  0  0  0  0  0  0  0  0
  -21.2470   -0.3669   -2.7855 H   0  0  0  0  0  0  0  0  0  0  0  0
  -19.6621   -0.0096   -3.6401 H   0  0  0  0  0  0  0  0  0  0  0  0
  -19.6864   -1.0824   -1.0263 H   0  0  0  0  0  0  0  0  0  0  0  0
  -19.6913    0.0607    1.3508 H   0  0  0  0  0  0  0  0  0  0  0  0
  -18.9489    1.4848    0.5248 H   0  0  0  0  0  0  0  0  0  0  0  0
  -17.6395   -1.2858    0.5614 H   0  0  0  0  0  0  0  0  0  0  0  0
  -17.0120    0.2296   -0.1493 H   0  0  0  0  0  0  0  0  0  0  0  0
  -17.2159    1.8505    3.3734 H   0  0  0  0  0  0  0  0  0  0  0  0
  -17.4778    2.2055    1.6682 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.7862    1.9586    2.2972 H   0  0  0  0  0  0  0  0  0  0  0  0
  -16.8520   -1.8299    2.5145 H   0  0  0  0  0  0  0  0  0  0  0  0
  -16.7591   -0.8631    4.9680 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.8917    0.5851    4.2335 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.9161   -2.2661    4.3145 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.3815   -0.9317    5.3630 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3335    0.8376    3.6325 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.0053    1.2697    3.9935 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.5328    1.1893    2.2809 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.5420   -2.5403    2.3573 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.9935    0.0637    1.6024 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.4246   -1.5871    1.3143 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.9766   -0.3715    0.0889 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.4286   -2.0542   -0.0993 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.7376   -1.1840   -2.4475 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.2167    0.4805   -2.7687 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.1606   -0.9637   -3.2003 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6202   -0.1947    0.0594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.7379    1.3323   -1.8579 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.8859    0.5893   -2.9917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6791   -1.6073   -2.7897 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7767   -0.2780   -3.6278 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1557   -2.0325   -3.1777 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0185   -1.5041   -1.9394 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2483   -2.8506   -1.5946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5344    0.5409   -0.1955 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2709   -1.5954    0.0458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1161   -0.7650    1.3476 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4050    0.8328   -0.5702 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1472    1.3270    0.9737 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7736   -0.3962    2.9182 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4727   -1.6136    2.7309 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0848    0.0129    3.3195 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3249    0.2716   -0.4428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4161   -1.0201    2.2690 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8373   -1.5580    0.6722 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2273    1.2232    1.8627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7612    0.6377    0.2416 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0266   -1.9723    3.3565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7235   -0.4440    3.8530 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0448   -0.5301    3.7974 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2030   -0.1972    0.1330 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5455   -2.2369    1.0359 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2950   -1.6544    2.6734 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5691   -1.0983    2.0688 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6199    0.3693    2.2946 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6393    1.5991    0.4299 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0714    2.0572   -0.4764 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8584    0.8791   -1.1919 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7920   -1.1788    0.0703 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3670   -0.5411   -2.4561 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0028    1.0957   -1.9393 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4250    1.2493   -1.0176 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2601    0.9227   -2.8190 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6684   -1.8014   -3.1239 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3640   -1.6193   -3.5397 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8773   -2.8156   -2.3108 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8745   -0.0412   -0.0104 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.4788   -2.8736   -1.1806 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3634   -2.5061    0.5470 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2981   -0.8950    0.2946 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.7484   -2.4744   -0.3836 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.1316   -2.3249   -3.2644 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.4361   -2.6170   -2.9148 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.7891   -1.2471   -3.9600 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.8117    0.7773   -0.9527 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3705    1.9418   -3.0866 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.7296    0.5345   -4.0785 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.6377    2.1807   -2.2849 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.6486    2.1324   -4.0518 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.2558   -0.4446   -4.9542 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.4849   -0.3350   -4.9802 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.2431   -1.6215   -4.0290 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.1953    0.8996   -1.3728 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.9009   -1.7392   -2.9139 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.0762   -1.5368   -1.1765 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.8267   -0.0693   -3.2287 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.1977   -1.5202   -2.2814 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.9387    1.9338   -0.1474 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.0363    2.0069   -2.0010 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.4485    2.3339   -1.0136 H   0  0  0  0  0  0  0  0  0  0  0  0
   19.2834   -1.1785   -0.4892 H   0  0  0  0  0  0  0  0  0  0  0  0
   19.2287   -0.0529    1.7959 H   0  0  0  0  0  0  0  0  0  0  0  0
   20.5472    0.6276    0.8185 H   0  0  0  0  0  0  0  0  0  0  0  0
   21.7245    2.1023    2.1468 H   0  0  0  0  0  0  0  0  0  0  0  0
   19.0191    0.8067    6.7630 H   0  0  0  0  0  0  0  0  0  0  0  0
   20.1280   -0.6194    4.8391 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
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M  END
Download

PDB for HMDB0012217 (Dodecaprenyl diphosphate)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       1.533 -32.037   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.866 -31.267   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.200 -32.037   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.866 -29.727   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.534 -31.267   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.867 -32.037   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.201 -31.267   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.535 -32.037   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.201 -29.727   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.868 -31.267   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.202 -32.037   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      13.536 -31.267   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      14.869 -32.037   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      13.536 -29.727   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      16.203 -31.267   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      17.537 -32.037   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      18.871 -31.267   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      20.204 -32.037   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      18.871 -29.727   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      21.538 -31.267   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      22.872 -32.037   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      24.205 -31.267   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      25.539 -32.037   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      24.205 -29.727   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      26.873 -31.267   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      28.207 -32.037   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      29.540 -31.267   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      30.874 -32.037   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      29.540 -29.727   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      32.208 -31.267   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      33.541 -32.037   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      34.875 -31.267   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      36.209 -32.037   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      34.875 -29.727   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      37.542 -31.267   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      38.876 -32.037   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      40.210 -31.267   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      41.543 -32.037   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      40.210 -29.727   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      42.877 -31.267   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      44.211 -32.037   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      45.545 -31.267   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      46.878 -32.037   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      45.545 -29.727   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      48.212 -31.267   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      49.546 -32.037   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      50.879 -31.267   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      52.213 -32.037   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      50.879 -29.727   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      53.547 -31.267   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      54.880 -32.037   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      56.214 -31.267   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      57.548 -32.037   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      56.214 -29.727   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      58.881 -31.267   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      60.215 -32.037   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      61.549 -31.267   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      62.883 -32.037   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      61.549 -29.727   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      64.216 -31.267   0.000  0.00  0.00           C+0
HETATM   61  O   UNK     0      65.550 -32.037   0.000  0.00  0.00           O+0
HETATM   62  P   UNK     0      66.884 -31.267   0.000  0.00  0.00           P+0
HETATM   63  O   UNK     0      66.114 -29.933   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0      68.217 -30.497   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0      67.654 -32.600   0.000  0.00  0.00           O+0
HETATM   66  P   UNK     0      68.217 -28.957   0.000  0.00  0.00           P+0
HETATM   67  O   UNK     0      69.757 -28.957   0.000  0.00  0.00           O+0
HETATM   68  O   UNK     0      66.677 -28.957   0.000  0.00  0.00           O+0
HETATM   69  O   UNK     0      68.217 -27.417   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2    5                                                       
CONECT    4    2                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7   10                                                       
CONECT    9    7                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12   15                                                       
CONECT   14   12                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17   20                                                       
CONECT   19   17                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22   25                                                       
CONECT   24   22                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27   30                                                       
CONECT   29   27                                                            
CONECT   30   28   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32   35                                                       
CONECT   34   32                                                            
CONECT   35   33   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38   39                                                  
CONECT   38   37   40                                                       
CONECT   39   37                                                            
CONECT   40   38   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43   44                                                  
CONECT   43   42   45                                                       
CONECT   44   42                                                            
CONECT   45   43   46                                                       
CONECT   46   45   47                                                       
CONECT   47   46   48   49                                                  
CONECT   48   47   50                                                       
CONECT   49   47                                                            
CONECT   50   48   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   53   54                                                  
CONECT   53   52   55                                                       
CONECT   54   52                                                            
CONECT   55   53   56                                                       
CONECT   56   55   57                                                       
CONECT   57   56   58   59                                                  
CONECT   58   57   60                                                       
CONECT   59   57                                                            
CONECT   60   58   61                                                       
CONECT   61   60   62                                                       
CONECT   62   63   64   65   61                                             
CONECT   63   62                                                            
CONECT   64   62   66                                                       
CONECT   65   62                                                            
CONECT   66   67   68   69   64                                             
CONECT   67   66                                                            
CONECT   68   66                                                            
CONECT   69   66                                                            
MASTER        0    0    0    0    0    0    0    0   69    0  136    0
END
Download

3D PDB for HMDB0012217 (Dodecaprenyl diphosphate)

COMPND    HMDB0012217
HETATM    1  C1  UNL     1     -19.796   2.304  -1.434  1.00  0.00           C  
HETATM    2  C2  UNL     1     -19.926   0.861  -1.687  1.00  0.00           C  
HETATM    3  C3  UNL     1     -20.486   0.418  -3.006  1.00  0.00           C  
HETATM    4  C4  UNL     1     -19.563  -0.030  -0.781  1.00  0.00           C  
HETATM    5  C5  UNL     1     -19.006   0.380   0.537  1.00  0.00           C  
HETATM    6  C6  UNL     1     -17.622  -0.183   0.689  1.00  0.00           C  
HETATM    7  C7  UNL     1     -17.017   0.175   2.028  1.00  0.00           C  
HETATM    8  C8  UNL     1     -16.841   1.605   2.355  1.00  0.00           C  
HETATM    9  C9  UNL     1     -16.670  -0.811   2.859  1.00  0.00           C  
HETATM   10  C10 UNL     1     -16.073  -0.498   4.173  1.00  0.00           C  
HETATM   11  C11 UNL     1     -14.736  -1.194   4.344  1.00  0.00           C  
HETATM   12  C12 UNL     1     -13.806  -0.712   3.304  1.00  0.00           C  
HETATM   13  C13 UNL     1     -13.383   0.720   3.261  1.00  0.00           C  
HETATM   14  C14 UNL     1     -13.284  -1.493   2.373  1.00  0.00           C  
HETATM   15  C15 UNL     1     -12.352  -0.952   1.355  1.00  0.00           C  
HETATM   16  C16 UNL     1     -13.062  -1.012   0.026  1.00  0.00           C  
HETATM   17  C17 UNL     1     -12.255  -0.532  -1.101  1.00  0.00           C  
HETATM   18  C18 UNL     1     -12.848  -0.496  -2.460  1.00  0.00           C  
HETATM   19  C19 UNL     1     -10.959  -0.121  -0.953  1.00  0.00           C  
HETATM   20  C20 UNL     1     -10.219   0.352  -2.135  1.00  0.00           C  
HETATM   21  C21 UNL     1      -9.180  -0.597  -2.613  1.00  0.00           C  
HETATM   22  C22 UNL     1      -8.085  -0.841  -1.692  1.00  0.00           C  
HETATM   23  C23 UNL     1      -7.052  -1.889  -2.087  1.00  0.00           C  
HETATM   24  C24 UNL     1      -7.878  -0.228  -0.517  1.00  0.00           C  
HETATM   25  C25 UNL     1      -6.712  -0.616   0.294  1.00  0.00           C  
HETATM   26  C26 UNL     1      -5.697   0.482   0.425  1.00  0.00           C  
HETATM   27  C27 UNL     1      -4.533  -0.077   1.208  1.00  0.00           C  
HETATM   28  C28 UNL     1      -4.729  -0.550   2.590  1.00  0.00           C  
HETATM   29  C29 UNL     1      -3.370  -0.115   0.604  1.00  0.00           C  
HETATM   30  C30 UNL     1      -2.163  -0.642   1.252  1.00  0.00           C  
HETATM   31  C31 UNL     1      -1.022   0.327   1.266  1.00  0.00           C  
HETATM   32  C32 UNL     1       0.161  -0.393   1.882  1.00  0.00           C  
HETATM   33  C33 UNL     1       0.117  -0.885   3.265  1.00  0.00           C  
HETATM   34  C34 UNL     1       1.244  -0.574   1.150  1.00  0.00           C  
HETATM   35  C35 UNL     1       2.448  -1.255   1.611  1.00  0.00           C  
HETATM   36  C36 UNL     1       3.730  -0.514   1.595  1.00  0.00           C  
HETATM   37  C37 UNL     1       4.148   0.048   0.301  1.00  0.00           C  
HETATM   38  C38 UNL     1       3.402   1.182  -0.290  1.00  0.00           C  
HETATM   39  C39 UNL     1       5.231  -0.380  -0.384  1.00  0.00           C  
HETATM   40  C40 UNL     1       5.636   0.201  -1.683  1.00  0.00           C  
HETATM   41  C41 UNL     1       7.091   0.530  -1.795  1.00  0.00           C  
HETATM   42  C42 UNL     1       7.881  -0.724  -1.674  1.00  0.00           C  
HETATM   43  C43 UNL     1       7.682  -1.802  -2.653  1.00  0.00           C  
HETATM   44  C44 UNL     1       8.752  -0.867  -0.711  1.00  0.00           C  
HETATM   45  C45 UNL     1       9.609  -2.051  -0.462  1.00  0.00           C  
HETATM   46  C46 UNL     1      11.054  -1.613  -0.491  1.00  0.00           C  
HETATM   47  C47 UNL     1      11.319  -1.016  -1.854  1.00  0.00           C  
HETATM   48  C48 UNL     1      11.179  -1.782  -3.097  1.00  0.00           C  
HETATM   49  C49 UNL     1      11.708   0.248  -1.927  1.00  0.00           C  
HETATM   50  C50 UNL     1      12.013   1.009  -3.140  1.00  0.00           C  
HETATM   51  C51 UNL     1      13.436   1.535  -3.165  1.00  0.00           C  
HETATM   52  C52 UNL     1      14.368   0.379  -3.163  1.00  0.00           C  
HETATM   53  C53 UNL     1      14.345  -0.575  -4.300  1.00  0.00           C  
HETATM   54  C54 UNL     1      15.254   0.177  -2.170  1.00  0.00           C  
HETATM   55  C55 UNL     1      16.173  -0.951  -2.159  1.00  0.00           C  
HETATM   56  C56 UNL     1      17.602  -0.575  -2.255  1.00  0.00           C  
HETATM   57  C57 UNL     1      18.015   0.303  -1.134  1.00  0.00           C  
HETATM   58  C58 UNL     1      17.506   1.685  -1.033  1.00  0.00           C  
HETATM   59  C59 UNL     1      18.909  -0.156  -0.284  1.00  0.00           C  
HETATM   60  C60 UNL     1      19.422   0.577   0.880  1.00  0.00           C  
HETATM   61  O1  UNL     1      18.906   1.839   1.074  1.00  0.00           O  
HETATM   62  P1  UNL     1      19.596   2.549   2.462  1.00  0.00           P  
HETATM   63  O2  UNL     1      19.861   4.021   2.209  1.00  0.00           O  
HETATM   64  O3  UNL     1      21.060   1.801   2.814  1.00  0.00           O  
HETATM   65  O4  UNL     1      18.527   2.455   3.770  1.00  0.00           O  
HETATM   66  P2  UNL     1      18.590   0.972   4.555  1.00  0.00           P  
HETATM   67  O5  UNL     1      17.550   0.053   3.968  1.00  0.00           O  
HETATM   68  O6  UNL     1      18.248   1.121   6.216  1.00  0.00           O  
HETATM   69  O7  UNL     1      20.117   0.243   4.368  1.00  0.00           O  
HETATM   70  H1  UNL     1     -18.738   2.649  -1.367  1.00  0.00           H  
HETATM   71  H2  UNL     1     -20.265   2.910  -2.247  1.00  0.00           H  
HETATM   72  H3  UNL     1     -20.291   2.630  -0.499  1.00  0.00           H  
HETATM   73  H4  UNL     1     -21.019   1.240  -3.526  1.00  0.00           H  
HETATM   74  H5  UNL     1     -21.247  -0.367  -2.785  1.00  0.00           H  
HETATM   75  H6  UNL     1     -19.662  -0.010  -3.640  1.00  0.00           H  
HETATM   76  H7  UNL     1     -19.686  -1.082  -1.026  1.00  0.00           H  
HETATM   77  H8  UNL     1     -19.691   0.061   1.351  1.00  0.00           H  
HETATM   78  H9  UNL     1     -18.949   1.485   0.525  1.00  0.00           H  
HETATM   79  H10 UNL     1     -17.639  -1.286   0.561  1.00  0.00           H  
HETATM   80  H11 UNL     1     -17.012   0.230  -0.149  1.00  0.00           H  
HETATM   81  H12 UNL     1     -17.216   1.851   3.373  1.00  0.00           H  
HETATM   82  H13 UNL     1     -17.478   2.206   1.668  1.00  0.00           H  
HETATM   83  H14 UNL     1     -15.786   1.959   2.297  1.00  0.00           H  
HETATM   84  H15 UNL     1     -16.852  -1.830   2.514  1.00  0.00           H  
HETATM   85  H16 UNL     1     -16.759  -0.863   4.968  1.00  0.00           H  
HETATM   86  H17 UNL     1     -15.892   0.585   4.234  1.00  0.00           H  
HETATM   87  H18 UNL     1     -14.916  -2.266   4.315  1.00  0.00           H  
HETATM   88  H19 UNL     1     -14.382  -0.932   5.363  1.00  0.00           H  
HETATM   89  H20 UNL     1     -12.334   0.838   3.633  1.00  0.00           H  
HETATM   90  H21 UNL     1     -14.005   1.270   3.994  1.00  0.00           H  
HETATM   91  H22 UNL     1     -13.533   1.189   2.281  1.00  0.00           H  
HETATM   92  H23 UNL     1     -13.542  -2.540   2.357  1.00  0.00           H  
HETATM   93  H24 UNL     1     -11.993   0.064   1.602  1.00  0.00           H  
HETATM   94  H25 UNL     1     -11.425  -1.587   1.314  1.00  0.00           H  
HETATM   95  H26 UNL     1     -13.977  -0.372   0.089  1.00  0.00           H  
HETATM   96  H27 UNL     1     -13.429  -2.054  -0.099  1.00  0.00           H  
HETATM   97  H28 UNL     1     -13.738  -1.184  -2.447  1.00  0.00           H  
HETATM   98  H29 UNL     1     -13.217   0.481  -2.769  1.00  0.00           H  
HETATM   99  H30 UNL     1     -12.161  -0.964  -3.200  1.00  0.00           H  
HETATM  100  H31 UNL     1     -10.620  -0.195   0.059  1.00  0.00           H  
HETATM  101  H32 UNL     1      -9.738   1.332  -1.858  1.00  0.00           H  
HETATM  102  H33 UNL     1     -10.886   0.589  -2.992  1.00  0.00           H  
HETATM  103  H34 UNL     1      -9.679  -1.607  -2.790  1.00  0.00           H  
HETATM  104  H35 UNL     1      -8.777  -0.278  -3.628  1.00  0.00           H  
HETATM  105  H36 UNL     1      -7.156  -2.033  -3.178  1.00  0.00           H  
HETATM  106  H37 UNL     1      -6.018  -1.504  -1.939  1.00  0.00           H  
HETATM  107  H38 UNL     1      -7.248  -2.851  -1.595  1.00  0.00           H  
HETATM  108  H39 UNL     1      -8.534   0.541  -0.196  1.00  0.00           H  
HETATM  109  H40 UNL     1      -6.271  -1.595   0.046  1.00  0.00           H  
HETATM  110  H41 UNL     1      -7.116  -0.765   1.348  1.00  0.00           H  
HETATM  111  H42 UNL     1      -5.405   0.833  -0.570  1.00  0.00           H  
HETATM  112  H43 UNL     1      -6.147   1.327   0.974  1.00  0.00           H  
HETATM  113  H44 UNL     1      -5.774  -0.396   2.918  1.00  0.00           H  
HETATM  114  H45 UNL     1      -4.473  -1.614   2.731  1.00  0.00           H  
HETATM  115  H46 UNL     1      -4.085   0.013   3.320  1.00  0.00           H  
HETATM  116  H47 UNL     1      -3.325   0.272  -0.443  1.00  0.00           H  
HETATM  117  H48 UNL     1      -2.416  -1.020   2.269  1.00  0.00           H  
HETATM  118  H49 UNL     1      -1.837  -1.558   0.672  1.00  0.00           H  
HETATM  119  H50 UNL     1      -1.227   1.223   1.863  1.00  0.00           H  
HETATM  120  H51 UNL     1      -0.761   0.638   0.242  1.00  0.00           H  
HETATM  121  H52 UNL     1       0.027  -1.972   3.357  1.00  0.00           H  
HETATM  122  H53 UNL     1      -0.724  -0.444   3.853  1.00  0.00           H  
HETATM  123  H54 UNL     1       1.045  -0.530   3.797  1.00  0.00           H  
HETATM  124  H55 UNL     1       1.203  -0.197   0.133  1.00  0.00           H  
HETATM  125  H56 UNL     1       2.545  -2.237   1.036  1.00  0.00           H  
HETATM  126  H57 UNL     1       2.295  -1.654   2.673  1.00  0.00           H  
HETATM  127  H58 UNL     1       4.569  -1.098   2.069  1.00  0.00           H  
HETATM  128  H59 UNL     1       3.620   0.369   2.295  1.00  0.00           H  
HETATM  129  H60 UNL     1       2.639   1.599   0.430  1.00  0.00           H  
HETATM  130  H61 UNL     1       4.071   2.057  -0.476  1.00  0.00           H  
HETATM  131  H62 UNL     1       2.858   0.879  -1.192  1.00  0.00           H  
HETATM  132  H63 UNL     1       5.792  -1.179   0.070  1.00  0.00           H  
HETATM  133  H64 UNL     1       5.367  -0.541  -2.456  1.00  0.00           H  
HETATM  134  H65 UNL     1       5.003   1.096  -1.939  1.00  0.00           H  
HETATM  135  H66 UNL     1       7.425   1.249  -1.018  1.00  0.00           H  
HETATM  136  H67 UNL     1       7.260   0.923  -2.819  1.00  0.00           H  
HETATM  137  H68 UNL     1       6.668  -1.801  -3.124  1.00  0.00           H  
HETATM  138  H69 UNL     1       8.364  -1.619  -3.540  1.00  0.00           H  
HETATM  139  H70 UNL     1       7.877  -2.816  -2.311  1.00  0.00           H  
HETATM  140  H71 UNL     1       8.875  -0.041  -0.010  1.00  0.00           H  
HETATM  141  H72 UNL     1       9.479  -2.874  -1.181  1.00  0.00           H  
HETATM  142  H73 UNL     1       9.363  -2.506   0.547  1.00  0.00           H  
HETATM  143  H74 UNL     1      11.298  -0.895   0.295  1.00  0.00           H  
HETATM  144  H75 UNL     1      11.748  -2.474  -0.384  1.00  0.00           H  
HETATM  145  H76 UNL     1      12.132  -2.325  -3.264  1.00  0.00           H  
HETATM  146  H77 UNL     1      10.436  -2.617  -2.915  1.00  0.00           H  
HETATM  147  H78 UNL     1      10.789  -1.247  -3.960  1.00  0.00           H  
HETATM  148  H79 UNL     1      11.812   0.777  -0.953  1.00  0.00           H  
HETATM  149  H80 UNL     1      11.371   1.942  -3.087  1.00  0.00           H  
HETATM  150  H81 UNL     1      11.730   0.535  -4.078  1.00  0.00           H  
HETATM  151  H82 UNL     1      13.638   2.181  -2.285  1.00  0.00           H  
HETATM  152  H83 UNL     1      13.649   2.132  -4.052  1.00  0.00           H  
HETATM  153  H84 UNL     1      15.256  -0.445  -4.954  1.00  0.00           H  
HETATM  154  H85 UNL     1      13.485  -0.335  -4.980  1.00  0.00           H  
HETATM  155  H86 UNL     1      14.243  -1.622  -4.029  1.00  0.00           H  
HETATM  156  H87 UNL     1      15.195   0.900  -1.373  1.00  0.00           H  
HETATM  157  H88 UNL     1      15.901  -1.739  -2.914  1.00  0.00           H  
HETATM  158  H89 UNL     1      16.076  -1.537  -1.177  1.00  0.00           H  
HETATM  159  H90 UNL     1      17.827  -0.069  -3.229  1.00  0.00           H  
HETATM  160  H91 UNL     1      18.198  -1.520  -2.281  1.00  0.00           H  
HETATM  161  H92 UNL     1      16.939   1.934  -0.147  1.00  0.00           H  
HETATM  162  H93 UNL     1      17.036   2.007  -2.001  1.00  0.00           H  
HETATM  163  H94 UNL     1      18.448   2.334  -1.014  1.00  0.00           H  
HETATM  164  H95 UNL     1      19.283  -1.179  -0.489  1.00  0.00           H  
HETATM  165  H96 UNL     1      19.229  -0.053   1.796  1.00  0.00           H  
HETATM  166  H97 UNL     1      20.547   0.628   0.819  1.00  0.00           H  
HETATM  167  H98 UNL     1      21.725   2.102   2.147  1.00  0.00           H  
HETATM  168  H99 UNL     1      19.019   0.807   6.763  1.00  0.00           H  
HETATM  169  HA0 UNL     1      20.128  -0.619   4.839  1.00  0.00           H  
CONECT    1    2   70   71   72
CONECT    2    3    4    4
CONECT    3   73   74   75
CONECT    4    5   76
CONECT    5    6   77   78
CONECT    6    7   79   80
CONECT    7    8    9    9
CONECT    8   81   82   83
CONECT    9   10   84
CONECT   10   11   85   86
CONECT   11   12   87   88
CONECT   12   13   14   14
CONECT   13   89   90   91
CONECT   14   15   92
CONECT   15   16   93   94
CONECT   16   17   95   96
CONECT   17   18   19   19
CONECT   18   97   98   99
CONECT   19   20  100
CONECT   20   21  101  102
CONECT   21   22  103  104
CONECT   22   23   24   24
CONECT   23  105  106  107
CONECT   24   25  108
CONECT   25   26  109  110
CONECT   26   27  111  112
CONECT   27   28   29   29
CONECT   28  113  114  115
CONECT   29   30  116
CONECT   30   31  117  118
CONECT   31   32  119  120
CONECT   32   33   34   34
CONECT   33  121  122  123
CONECT   34   35  124
CONECT   35   36  125  126
CONECT   36   37  127  128
CONECT   37   38   39   39
CONECT   38  129  130  131
CONECT   39   40  132
CONECT   40   41  133  134
CONECT   41   42  135  136
CONECT   42   43   44   44
CONECT   43  137  138  139
CONECT   44   45  140
CONECT   45   46  141  142
CONECT   46   47  143  144
CONECT   47   48   49   49
CONECT   48  145  146  147
CONECT   49   50  148
CONECT   50   51  149  150
CONECT   51   52  151  152
CONECT   52   53   54   54
CONECT   53  153  154  155
CONECT   54   55  156
CONECT   55   56  157  158
CONECT   56   57  159  160
CONECT   57   58   59   59
CONECT   58  161  162  163
CONECT   59   60  164
CONECT   60   61  165  166
CONECT   61   62
CONECT   62   63   63   64   65
CONECT   64  167
CONECT   65   66
CONECT   66   67   67   68   69
CONECT   68  168
CONECT   69  169
END
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SMILES for HMDB0012217 (Dodecaprenyl diphosphate)

CC(C)=CCC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\COP(O)(=O)OP(O)(O)=O
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INCHI for HMDB0012217 (Dodecaprenyl diphosphate)

InChI=1S/C60H100O7P2/c1-49(2)25-14-26-50(3)27-15-28-51(4)29-16-30-52(5)31-17-32-53(6)33-18-34-54(7)35-19-36-55(8)37-20-38-56(9)39-21-40-57(10)41-22-42-58(11)43-23-44-59(12)45-24-46-60(13)47-48-66-69(64,65)67-68(61,62)63/h25,27,29,31,33,35,37,39,41,43,45,47H,14-24,26,28,30,32,34,36,38,40,42,44,46,48H2,1-13H3,(H,64,65)(H2,61,62,63)/b50-27+,51-29+,52-31+,53-33+,54-35+,55-37+,56-39+,57-41+,58-43+,59-45+,60-47+
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View in JSmolView Stereo Labels
Synonyms
ValueSource
all-trans-Dodecaprenyl pyrophosphateChEBI
all-trans-Dodecaprenyl pyrophosphoric acidGenerator
Dodecaprenyl diphosphoric acidGenerator
all-trans-Dodecaprenyl diphosphateHMDB
all-trans-Dodecaprenyl diphosphoric acidGenerator, HMDB
Chemical FormulaC60H100O7P2
Average Molecular Weight995.3793
Monoisotopic Molecular Weight994.694428578
IUPAC Name[({[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E,42E)-3,7,11,15,19,23,27,31,35,39,43,47-dodecamethyloctatetraconta-2,6,10,14,18,22,26,30,34,38,42,46-dodecaen-1-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional Name{[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E,42E)-3,7,11,15,19,23,27,31,35,39,43,47-dodecamethyloctatetraconta-2,6,10,14,18,22,26,30,34,38,42,46-dodecaen-1-yl]oxy(hydroxy)phosphoryl}oxyphosphonic acid
CAS Registry NumberNot Available
SMILES
CC(C)=CCC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\CC\C(C)=C\COP(O)(=O)OP(O)(O)=O
InChI Identifier
InChI=1S/C60H100O7P2/c1-49(2)25-14-26-50(3)27-15-28-51(4)29-16-30-52(5)31-17-32-53(6)33-18-34-54(7)35-19-36-55(8)37-20-38-56(9)39-21-40-57(10)41-22-42-58(11)43-23-44-59(12)45-24-46-60(13)47-48-66-69(64,65)67-68(61,62)63/h25,27,29,31,33,35,37,39,41,43,45,47H,14-24,26,28,30,32,34,36,38,40,42,44,46,48H2,1-13H3,(H,64,65)(H2,61,62,63)/b50-27+,51-29+,52-31+,53-33+,54-35+,55-37+,56-39+,57-41+,58-43+,59-45+,60-47+
InChI KeyWURMRKUXTPWSRM-GNZYJLLNSA-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 roleIndustrial application
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 Solubility0.00038 g/LALOGPS
logP9.58ALOGPS
logP18.55ChemAxon
logS-6.4ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area113.29 ŲChemAxon
Rotatable Bond Count38ChemAxon
Refractivity310.95 m³·mol⁻¹ChemAxon
Polarizability124.6 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
DeepCCS[M+H]+328.66130932474
DeepCCS[M-H]-326.91930932474
DeepCCS[M-2H]-360.95330932474
DeepCCS[M+Na]+334.97230932474
AllCCS[M+H]+295.832859911
AllCCS[M+H-H2O]+295.432859911
AllCCS[M+NH4]+296.232859911
AllCCS[M+Na]+296.332859911
AllCCS[M-H]-208.932859911
AllCCS[M+Na-2H]-209.932859911
AllCCS[M+HCOO]-210.932859911

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, 2022.3.52 minutes32390414
Predicted by Siyang on May 30, 202242.5043 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20221.96 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid110.8 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid7158.3 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid629.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid502.4 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid325.5 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid305.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1939.4 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 Acid1970.3 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)152.0 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid4068.9 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid1691.1 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1476.1 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1629.5 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid726.9 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate243.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA1086.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water12.5 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dodecaprenyl diphosphate 10V, Positive-QTOFsplash10-014i-0100000189-2edc9d188cdd471bc22d2016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dodecaprenyl diphosphate 20V, Positive-QTOFsplash10-014i-1000000091-c01144251fbef1de46db2016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dodecaprenyl diphosphate 40V, Positive-QTOFsplash10-014i-0012111290-b0f452e7ff7177adaf652016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dodecaprenyl diphosphate 10V, Negative-QTOFsplash10-0006-0400000009-e78be2fb2c5c99228e4c2016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dodecaprenyl diphosphate 20V, Negative-QTOFsplash10-056r-7900000001-22af3cae09bb65bbe8bf2016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dodecaprenyl diphosphate 40V, Negative-QTOFsplash10-004i-9000000000-0a08fe4d6f7ad13c80672016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dodecaprenyl diphosphate 10V, Negative-QTOFsplash10-0006-0000000009-524bfdbc14cd3a33f8402021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dodecaprenyl diphosphate 20V, Negative-QTOFsplash10-002f-2200000019-df2e9591617a6795bbe32021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dodecaprenyl diphosphate 40V, Negative-QTOFsplash10-004i-9100000000-8639d2f0aded471437872021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dodecaprenyl diphosphate 10V, Positive-QTOFsplash10-0002-0100000049-9f643bc70c3d7c79380f2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dodecaprenyl diphosphate 20V, Positive-QTOFsplash10-01b9-0001001192-d2149a914b0ea28a6d1e2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dodecaprenyl diphosphate 40V, Positive-QTOFsplash10-0gc0-0219567352-4d159ec78f94c1fd85e82021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
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 IDFDB028861
KNApSAcK IDNot Available
Chemspider ID34999496
KEGG Compound IDNot Available
BioCyc IDCPD-9650
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound25246061
PDB IDNot Available
ChEBI ID84599
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.