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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (4) Show 4 proteins XML

Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2006-08-12 23:33:54 UTC

Update Date

2022-03-07 02:49:19 UTC

HMDB ID

HMDB0003550

Secondary Accession Numbers

HMDB0005997
HMDB03550
HMDB05997

Metabolite Identification

Common Name

Calcidiol

Description

Calcidiol, also known as 25(OH)D3 or rayaldee, belongs to the class of organic compounds known as vitamin d and derivatives. Vitamin D and derivatives are compounds containing a secosteroid backbone, usually secoergostane or secocholestane. Thus, calcidiol is considered to be a secosteroid lipid molecule. Calcidiol is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Calcidiol is a potentially toxic compound.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv0541 04191212102D          

 31 33  0  0  1  0            999 V2000
   -1.0890    1.2765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0890   -0.3735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4101   -0.2159    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8950    0.4515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8035    0.8640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0890   -1.1985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8035    0.0390    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8035   -1.6110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8035   -2.4360    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0890   -2.8485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5179   -2.8485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0890   -3.6735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3745   -2.4360    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5179   -3.6735    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8035   -4.0860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2324   -4.0860    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3044    2.3565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4101    1.9440    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1246    2.3565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8390    1.9440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9825    2.3565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2680    1.1190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5535    2.3565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4101    1.1190    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1246    1.5315    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3745    0.0390    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3745   -0.7860    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3745    0.8640    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3745    1.6890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2680    1.9440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9825    1.5315    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 26 28  1  0  0  0  0
 28 24  1  0  0  0  0
 28  1  1  0  0  0  0
 26  2  1  0  0  0  0
 26  3  1  0  0  0  0
 24  4  1  0  0  0  0
  1  5  1  0  0  0  0
  2  6  2  0  0  0  0
  2  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 10 13  2  0  0  0  0
 11 14  1  0  0  0  0
 12 15  1  0  0  0  0
 14 16  1  6  0  0  0
  3  4  1  0  0  0  0
  5  7  1  0  0  0  0
 14 15  1  0  0  0  0
 24 18  1  0  0  0  0
 18 17  1  6  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 23  1  0  0  0  0
 23 30  1  0  0  0  0
 30 21  1  0  0  0  0
 30 22  1  0  0  0  0
 24 25  1  6  0  0  0
 26 27  1  6  0  0  0
 28 29  1  1  0  0  0
 30 31  1  0  0  0  0
M  END

HMDB0003550
     RDKit          3D
Calcidiol
 73 75  0  0  0  0  0  0  0  0999 V2000
    3.2122    1.5891   -1.9210 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4236    1.2310   -1.6293 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4445    0.9910   -2.7161 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8316    1.0841   -2.0808 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8260    2.1225   -0.9881 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.1581    2.4138   -0.6917 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0703    1.6431    0.2451 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7920    1.0561   -0.2376 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9649    0.3285    0.5174 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7559   -0.2954    0.0376 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0037   -0.9446    0.8880 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4278   -1.0090    2.3134 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3094   -1.7031    3.0604 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0455   -1.1318    2.8123 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3585   -0.8732    1.3553 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1578    0.5425    1.0707 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7517   -1.6379    0.5852 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2343   -1.5368   -0.7969 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2193   -1.9104   -0.6296 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5058   -1.6248    0.8305 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8852   -1.2864    1.1528 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.7390   -2.3379    0.4177 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4380    0.0420    1.1456 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5188    0.9561    0.0258 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3230    0.6548   -1.1777 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8069    0.5421   -0.9297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3307    1.8648   -0.3728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5104    0.3105   -2.2518 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2058   -0.4305   -0.0669 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9502    1.7070   -2.9831 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4639    1.8160   -1.1840 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3002   -0.0552   -3.0427 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3279    1.6620   -3.5664 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1389    0.1007   -1.6626 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5678    1.3748   -2.8392 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3350    3.0392   -1.3981 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2248    2.6108    0.2943 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9293    2.5138    0.8957 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7094    0.8719    0.7278 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2770    0.2301    1.5718 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4597   -0.3133   -0.9721 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6681   -0.0219    2.7517 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3314   -1.6399    2.4135 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3947   -2.7887    2.8350 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249   -1.6115    4.1519 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2018   -0.2309    3.4419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7904   -1.9030    3.1503 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7027    1.2078    1.8043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2441    0.8896    0.0365 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9258    0.7798    1.3216 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7917   -2.6836    0.8897 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7549   -2.2942   -1.4525 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3396   -0.5390   -1.2708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8910   -1.3722   -1.3137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3062   -2.9810   -0.9069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3653   -2.6645    1.2951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0394   -1.6381    2.2395 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2154   -3.3416    0.5400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7190   -2.1667   -0.6595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7085   -2.4870    0.8883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5162   -0.0795    1.5206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0001    0.6169    2.0271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5304    1.4584   -0.2419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0511    1.8871    0.4542 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2302    1.5800   -1.8456 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9579   -0.1529   -1.8353 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1317    1.8559    0.7373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8543    2.7262   -0.8534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4385    1.9231   -0.4710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8496    1.2805   -2.6630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8709   -0.2491   -2.9735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4367   -0.3070   -2.0998 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5252   -1.2611   -0.5036 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  1
 15 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 21 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  1  0
 26 28  1  0
 26 29  1  0
  8  2  1  0
 17 11  1  0
 20 15  1  0
  1 30  1  0
  1 31  1  0
  3 32  1  0
  3 33  1  0
  4 34  1  0
  4 35  1  0
  5 36  1  6
  6 37  1  0
  7 38  1  0
  7 39  1  0
  9 40  1  0
 10 41  1  0
 12 42  1  0
 12 43  1  0
 13 44  1  0
 13 45  1  0
 14 46  1  0
 14 47  1  0
 16 48  1  0
 16 49  1  0
 16 50  1  0
 17 51  1  1
 18 52  1  0
 18 53  1  0
 19 54  1  0
 19 55  1  0
 20 56  1  1
 21 57  1  1
 22 58  1  0
 22 59  1  0
 22 60  1  0
 23 61  1  0
 23 62  1  0
 24 63  1  0
 24 64  1  0
 25 65  1  0
 25 66  1  0
 27 67  1  0
 27 68  1  0
 27 69  1  0
 28 70  1  0
 28 71  1  0
 28 72  1  0
 29 73  1  0
M  END


  Mrv0541 04191212102D          

 31 33  0  0  1  0            999 V2000
   -1.0890    1.2765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0890   -0.3735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4101   -0.2159    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8950    0.4515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8035    0.8640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0890   -1.1985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8035    0.0390    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8035   -1.6110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8035   -2.4360    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0890   -2.8485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5179   -2.8485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0890   -3.6735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3745   -2.4360    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5179   -3.6735    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8035   -4.0860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2324   -4.0860    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3044    2.3565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4101    1.9440    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1246    2.3565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8390    1.9440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9825    2.3565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2680    1.1190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5535    2.3565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4101    1.1190    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1246    1.5315    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3745    0.0390    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3745   -0.7860    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3745    0.8640    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3745    1.6890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2680    1.9440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9825    1.5315    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 26 28  1  0  0  0  0
 28 24  1  0  0  0  0
 28  1  1  0  0  0  0
 26  2  1  0  0  0  0
 26  3  1  0  0  0  0
 24  4  1  0  0  0  0
  1  5  1  0  0  0  0
  2  6  2  0  0  0  0
  2  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 10 13  2  0  0  0  0
 11 14  1  0  0  0  0
 12 15  1  0  0  0  0
 14 16  1  6  0  0  0
  3  4  1  0  0  0  0
  5  7  1  0  0  0  0
 14 15  1  0  0  0  0
 24 18  1  0  0  0  0
 18 17  1  6  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 23  1  0  0  0  0
 23 30  1  0  0  0  0
 30 21  1  0  0  0  0
 30 22  1  0  0  0  0
 24 25  1  6  0  0  0
 26 27  1  6  0  0  0
 28 29  1  1  0  0  0
 30 31  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0003550

> <DATABASE_NAME>
hmdb

> <SMILES>
C[C@H](CCCC(C)(C)O)[C@@]1([H])CC[C@@]2([H])\C(CCC[C@]12C)=C\C=C1\C[C@@H](O)CCC1=C

> <INCHI_IDENTIFIER>
InChI=1S/C27H44O2/c1-19-10-13-23(28)18-22(19)12-11-21-9-7-17-27(5)24(14-15-25(21)27)20(2)8-6-16-26(3,4)29/h11-12,20,23-25,28-29H,1,6-10,13-18H2,2-5H3/b21-11+,22-12-/t20-,23+,24-,25+,27-/m1/s1

> <INCHI_KEY>
JWUBBDSIWDLEOM-DTOXIADCSA-N

> <FORMULA>
C27H44O2

> <MOLECULAR_WEIGHT>
400.6371

> <EXACT_MASS>
400.334130652

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
50.319516931050124

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,3Z)-3-{2-[(1R,3aS,4E,7aR)-1-[(2R)-6-hydroxy-6-methylheptan-2-yl]-7a-methyl-octahydro-1H-inden-4-ylidene]ethylidene}-4-methylidenecyclohexan-1-ol

> <ALOGPS_LOGP>
6.71

> <JCHEM_LOGP>
5.654346069666669

> <ALOGPS_LOGS>
-5.26

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.53076846661296

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.384341369959035

> <JCHEM_PKA_STRONGEST_BASIC>
-0.9842558878714639

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
125.06059999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.20e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
25-hydroxyvitamin D3

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0003550
     RDKit          3D
Calcidiol
 73 75  0  0  0  0  0  0  0  0999 V2000
    3.2122    1.5891   -1.9210 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4236    1.2310   -1.6293 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4445    0.9910   -2.7161 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8316    1.0841   -2.0808 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8260    2.1225   -0.9881 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.1581    2.4138   -0.6917 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0703    1.6431    0.2451 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7920    1.0561   -0.2376 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9649    0.3285    0.5174 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7559   -0.2954    0.0376 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0037   -0.9446    0.8880 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4278   -1.0090    2.3134 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3094   -1.7031    3.0604 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0455   -1.1318    2.8123 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3585   -0.8732    1.3553 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1578    0.5425    1.0707 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7517   -1.6379    0.5852 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2343   -1.5368   -0.7969 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2193   -1.9104   -0.6296 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5058   -1.6248    0.8305 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8852   -1.2864    1.1528 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.7390   -2.3379    0.4177 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4380    0.0420    1.1456 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5188    0.9561    0.0258 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3230    0.6548   -1.1777 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8069    0.5421   -0.9297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3307    1.8648   -0.3728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5104    0.3105   -2.2518 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2058   -0.4305   -0.0669 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9502    1.7070   -2.9831 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4639    1.8160   -1.1840 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3002   -0.0552   -3.0427 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3279    1.6620   -3.5664 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1389    0.1007   -1.6626 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5678    1.3748   -2.8392 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3350    3.0392   -1.3981 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2248    2.6108    0.2943 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9293    2.5138    0.8957 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7094    0.8719    0.7278 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2770    0.2301    1.5718 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4597   -0.3133   -0.9721 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6681   -0.0219    2.7517 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3314   -1.6399    2.4135 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3947   -2.7887    2.8350 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249   -1.6115    4.1519 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2018   -0.2309    3.4419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7904   -1.9030    3.1503 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7027    1.2078    1.8043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2441    0.8896    0.0365 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9258    0.7798    1.3216 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7917   -2.6836    0.8897 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7549   -2.2942   -1.4525 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3396   -0.5390   -1.2708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8910   -1.3722   -1.3137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3062   -2.9810   -0.9069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3653   -2.6645    1.2951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0394   -1.6381    2.2395 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2154   -3.3416    0.5400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7190   -2.1667   -0.6595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7085   -2.4870    0.8883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5162   -0.0795    1.5206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0001    0.6169    2.0271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5304    1.4584   -0.2419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0511    1.8871    0.4542 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2302    1.5800   -1.8456 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9579   -0.1529   -1.8353 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1317    1.8559    0.7373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8543    2.7262   -0.8534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4385    1.9231   -0.4710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8496    1.2805   -2.6630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8709   -0.2491   -2.9735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4367   -0.3070   -2.0998 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5252   -1.2611   -0.5036 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  1
 15 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 21 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  1  0
 26 28  1  0
 26 29  1  0
  8  2  1  0
 17 11  1  0
 20 15  1  0
  1 30  1  0
  1 31  1  0
  3 32  1  0
  3 33  1  0
  4 34  1  0
  4 35  1  0
  5 36  1  6
  6 37  1  0
  7 38  1  0
  7 39  1  0
  9 40  1  0
 10 41  1  0
 12 42  1  0
 12 43  1  0
 13 44  1  0
 13 45  1  0
 14 46  1  0
 14 47  1  0
 16 48  1  0
 16 49  1  0
 16 50  1  0
 17 51  1  1
 18 52  1  0
 18 53  1  0
 19 54  1  0
 19 55  1  0
 20 56  1  1
 21 57  1  1
 22 58  1  0
 22 59  1  0
 22 60  1  0
 23 61  1  0
 23 62  1  0
 24 63  1  0
 24 64  1  0
 25 65  1  0
 25 66  1  0
 27 67  1  0
 27 68  1  0
 27 69  1  0
 28 70  1  0
 28 71  1  0
 28 72  1  0
 29 73  1  0
M  END

HEADER    PROTEIN                                 19-APR-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-12         0                                  
HETATM    1  C   UNK     0      -2.033   2.383   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.033  -0.697   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.766  -0.403   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.671   0.843   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.367   1.613   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.033  -2.237   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.367   0.073   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.367  -3.007   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.367  -4.547   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.033  -5.317   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -4.700  -5.317   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.033  -6.857   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.699  -4.547   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.700  -6.857   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -3.367  -7.627   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -6.034  -7.627   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -0.568   4.399   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.766   3.629   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.099   4.399   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.433   3.629   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.434   4.399   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.100   2.089   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.767   4.399   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.766   2.089   0.000  0.00  0.00           C+0
HETATM   25  H   UNK     0       2.099   2.859   0.000  0.00  0.00           H+0
HETATM   26  C   UNK     0      -0.699   0.073   0.000  0.00  0.00           C+0
HETATM   27  H   UNK     0      -0.699  -1.467   0.000  0.00  0.00           H+0
HETATM   28  C   UNK     0      -0.699   1.613   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -0.699   3.153   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.100   3.629   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       7.434   2.859   0.000  0.00  0.00           O+0
CONECT    1   28    5                                                       
CONECT    2   26    6    7                                                  
CONECT    3   26    4                                                       
CONECT    4   24    3                                                       
CONECT    5    1    7                                                       
CONECT    6    2    8                                                       
CONECT    7    2    5                                                       
CONECT    8    6    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9   12   13                                                  
CONECT   11    9   14                                                       
CONECT   12   10   15                                                       
CONECT   13   10                                                            
CONECT   14   11   16   15                                                  
CONECT   15   12   14                                                       
CONECT   16   14                                                            
CONECT   17   18                                                            
CONECT   18   24   17   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19   23                                                       
CONECT   21   30                                                            
CONECT   22   30                                                            
CONECT   23   20   30                                                       
CONECT   24   28    4   18   25                                             
CONECT   25   24                                                            
CONECT   26   28    2    3   27                                             
CONECT   27   26                                                            
CONECT   28   26   24    1   29                                             
CONECT   29   28                                                            
CONECT   30   23   21   22   31                                             
CONECT   31   30                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   66    0
END

COMPND    HMDB0003550
HETATM    1  C1  UNL     1       3.212   1.589  -1.921  1.00  0.00           C  
HETATM    2  C2  UNL     1       4.424   1.231  -1.629  1.00  0.00           C  
HETATM    3  C3  UNL     1       5.445   0.991  -2.716  1.00  0.00           C  
HETATM    4  C4  UNL     1       6.832   1.084  -2.081  1.00  0.00           C  
HETATM    5  C5  UNL     1       6.826   2.123  -0.988  1.00  0.00           C  
HETATM    6  O1  UNL     1       8.158   2.414  -0.692  1.00  0.00           O  
HETATM    7  C6  UNL     1       6.070   1.643   0.245  1.00  0.00           C  
HETATM    8  C7  UNL     1       4.792   1.056  -0.238  1.00  0.00           C  
HETATM    9  C8  UNL     1       3.965   0.329   0.517  1.00  0.00           C  
HETATM   10  C9  UNL     1       2.756  -0.295   0.038  1.00  0.00           C  
HETATM   11  C10 UNL     1       2.004  -0.945   0.888  1.00  0.00           C  
HETATM   12  C11 UNL     1       2.428  -1.009   2.313  1.00  0.00           C  
HETATM   13  C12 UNL     1       1.309  -1.703   3.060  1.00  0.00           C  
HETATM   14  C13 UNL     1      -0.045  -1.132   2.812  1.00  0.00           C  
HETATM   15  C14 UNL     1      -0.358  -0.873   1.355  1.00  0.00           C  
HETATM   16  C15 UNL     1      -0.158   0.543   1.071  1.00  0.00           C  
HETATM   17  C16 UNL     1       0.752  -1.638   0.585  1.00  0.00           C  
HETATM   18  C17 UNL     1       0.234  -1.537  -0.797  1.00  0.00           C  
HETATM   19  C18 UNL     1      -1.219  -1.910  -0.630  1.00  0.00           C  
HETATM   20  C19 UNL     1      -1.506  -1.625   0.831  1.00  0.00           C  
HETATM   21  C20 UNL     1      -2.885  -1.286   1.153  1.00  0.00           C  
HETATM   22  C21 UNL     1      -3.739  -2.338   0.418  1.00  0.00           C  
HETATM   23  C22 UNL     1      -3.438   0.042   1.146  1.00  0.00           C  
HETATM   24  C23 UNL     1      -3.519   0.956   0.026  1.00  0.00           C  
HETATM   25  C24 UNL     1      -4.323   0.655  -1.178  1.00  0.00           C  
HETATM   26  C25 UNL     1      -5.807   0.542  -0.930  1.00  0.00           C  
HETATM   27  C26 UNL     1      -6.331   1.865  -0.373  1.00  0.00           C  
HETATM   28  C27 UNL     1      -6.510   0.310  -2.252  1.00  0.00           C  
HETATM   29  O2  UNL     1      -6.206  -0.430  -0.067  1.00  0.00           O  
HETATM   30  H1  UNL     1       2.950   1.707  -2.983  1.00  0.00           H  
HETATM   31  H2  UNL     1       2.464   1.816  -1.184  1.00  0.00           H  
HETATM   32  H3  UNL     1       5.300  -0.055  -3.043  1.00  0.00           H  
HETATM   33  H4  UNL     1       5.328   1.662  -3.566  1.00  0.00           H  
HETATM   34  H5  UNL     1       7.139   0.101  -1.663  1.00  0.00           H  
HETATM   35  H6  UNL     1       7.568   1.375  -2.839  1.00  0.00           H  
HETATM   36  H7  UNL     1       6.335   3.039  -1.398  1.00  0.00           H  
HETATM   37  H8  UNL     1       8.225   2.611   0.294  1.00  0.00           H  
HETATM   38  H9  UNL     1       5.929   2.514   0.896  1.00  0.00           H  
HETATM   39  H10 UNL     1       6.709   0.872   0.728  1.00  0.00           H  
HETATM   40  H11 UNL     1       4.277   0.230   1.572  1.00  0.00           H  
HETATM   41  H12 UNL     1       2.460  -0.313  -0.972  1.00  0.00           H  
HETATM   42  H13 UNL     1       2.668  -0.022   2.752  1.00  0.00           H  
HETATM   43  H14 UNL     1       3.331  -1.640   2.414  1.00  0.00           H  
HETATM   44  H15 UNL     1       1.395  -2.789   2.835  1.00  0.00           H  
HETATM   45  H16 UNL     1       1.525  -1.612   4.152  1.00  0.00           H  
HETATM   46  H17 UNL     1      -0.202  -0.231   3.442  1.00  0.00           H  
HETATM   47  H18 UNL     1      -0.790  -1.903   3.150  1.00  0.00           H  
HETATM   48  H19 UNL     1      -0.703   1.208   1.804  1.00  0.00           H  
HETATM   49  H20 UNL     1      -0.244   0.890   0.036  1.00  0.00           H  
HETATM   50  H21 UNL     1       0.926   0.780   1.322  1.00  0.00           H  
HETATM   51  H22 UNL     1       0.792  -2.684   0.890  1.00  0.00           H  
HETATM   52  H23 UNL     1       0.755  -2.294  -1.453  1.00  0.00           H  
HETATM   53  H24 UNL     1       0.340  -0.539  -1.271  1.00  0.00           H  
HETATM   54  H25 UNL     1      -1.891  -1.372  -1.314  1.00  0.00           H  
HETATM   55  H26 UNL     1      -1.306  -2.981  -0.907  1.00  0.00           H  
HETATM   56  H27 UNL     1      -1.365  -2.664   1.295  1.00  0.00           H  
HETATM   57  H28 UNL     1      -3.039  -1.638   2.240  1.00  0.00           H  
HETATM   58  H29 UNL     1      -3.215  -3.342   0.540  1.00  0.00           H  
HETATM   59  H30 UNL     1      -3.719  -2.167  -0.659  1.00  0.00           H  
HETATM   60  H31 UNL     1      -4.709  -2.487   0.888  1.00  0.00           H  
HETATM   61  H32 UNL     1      -4.516  -0.080   1.521  1.00  0.00           H  
HETATM   62  H33 UNL     1      -3.000   0.617   2.027  1.00  0.00           H  
HETATM   63  H34 UNL     1      -2.530   1.458  -0.242  1.00  0.00           H  
HETATM   64  H35 UNL     1      -4.051   1.887   0.454  1.00  0.00           H  
HETATM   65  H36 UNL     1      -4.230   1.580  -1.846  1.00  0.00           H  
HETATM   66  H37 UNL     1      -3.958  -0.153  -1.835  1.00  0.00           H  
HETATM   67  H38 UNL     1      -6.132   1.856   0.737  1.00  0.00           H  
HETATM   68  H39 UNL     1      -5.854   2.726  -0.853  1.00  0.00           H  
HETATM   69  H40 UNL     1      -7.438   1.923  -0.471  1.00  0.00           H  
HETATM   70  H41 UNL     1      -6.850   1.280  -2.663  1.00  0.00           H  
HETATM   71  H42 UNL     1      -5.871  -0.249  -2.973  1.00  0.00           H  
HETATM   72  H43 UNL     1      -7.437  -0.307  -2.100  1.00  0.00           H  
HETATM   73  H44 UNL     1      -6.525  -1.261  -0.504  1.00  0.00           H  
CONECT    1    2    2   30   31
CONECT    2    3    8
CONECT    3    4   32   33
CONECT    4    5   34   35
CONECT    5    6    7   36
CONECT    6   37
CONECT    7    8   38   39
CONECT    8    9    9
CONECT    9   10   40
CONECT   10   11   11   41
CONECT   11   12   17
CONECT   12   13   42   43
CONECT   13   14   44   45
CONECT   14   15   46   47
CONECT   15   16   17   20
CONECT   16   48   49   50
CONECT   17   18   51
CONECT   18   19   52   53
CONECT   19   20   54   55
CONECT   20   21   56
CONECT   21   22   23   57
CONECT   22   58   59   60
CONECT   23   24   61   62
CONECT   24   25   63   64
CONECT   25   26   65   66
CONECT   26   27   28   29
CONECT   27   67   68   69
CONECT   28   70   71   72
CONECT   29   73
END

HMDB0003550
     RDKit          3D
Calcidiol
 73 75  0  0  0  0  0  0  0  0999 V2000
    3.2122    1.5891   -1.9210 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4236    1.2310   -1.6293 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4445    0.9910   -2.7161 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8316    1.0841   -2.0808 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8260    2.1225   -0.9881 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.1581    2.4138   -0.6917 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0703    1.6431    0.2451 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7920    1.0561   -0.2376 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9649    0.3285    0.5174 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7559   -0.2954    0.0376 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0037   -0.9446    0.8880 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4278   -1.0090    2.3134 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3094   -1.7031    3.0604 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0455   -1.1318    2.8123 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3585   -0.8732    1.3553 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1578    0.5425    1.0707 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7517   -1.6379    0.5852 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2343   -1.5368   -0.7969 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2193   -1.9104   -0.6296 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5058   -1.6248    0.8305 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8852   -1.2864    1.1528 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.7390   -2.3379    0.4177 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4380    0.0420    1.1456 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5188    0.9561    0.0258 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3230    0.6548   -1.1777 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8069    0.5421   -0.9297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3307    1.8648   -0.3728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5104    0.3105   -2.2518 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2058   -0.4305   -0.0669 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9502    1.7070   -2.9831 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4639    1.8160   -1.1840 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3002   -0.0552   -3.0427 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3279    1.6620   -3.5664 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1389    0.1007   -1.6626 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5678    1.3748   -2.8392 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3350    3.0392   -1.3981 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2248    2.6108    0.2943 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9293    2.5138    0.8957 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7094    0.8719    0.7278 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2770    0.2301    1.5718 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4597   -0.3133   -0.9721 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6681   -0.0219    2.7517 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3314   -1.6399    2.4135 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3947   -2.7887    2.8350 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249   -1.6115    4.1519 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2018   -0.2309    3.4419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7904   -1.9030    3.1503 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7027    1.2078    1.8043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2441    0.8896    0.0365 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9258    0.7798    1.3216 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7917   -2.6836    0.8897 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7549   -2.2942   -1.4525 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3396   -0.5390   -1.2708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8910   -1.3722   -1.3137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3062   -2.9810   -0.9069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3653   -2.6645    1.2951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0394   -1.6381    2.2395 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2154   -3.3416    0.5400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7190   -2.1667   -0.6595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7085   -2.4870    0.8883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5162   -0.0795    1.5206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0001    0.6169    2.0271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5304    1.4584   -0.2419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0511    1.8871    0.4542 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2302    1.5800   -1.8456 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9579   -0.1529   -1.8353 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1317    1.8559    0.7373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8543    2.7262   -0.8534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4385    1.9231   -0.4710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8496    1.2805   -2.6630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8709   -0.2491   -2.9735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4367   -0.3070   -2.0998 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5252   -1.2611   -0.5036 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  1
 15 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 21 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  1  0
 26 28  1  0
 26 29  1  0
  8  2  1  0
 17 11  1  0
 20 15  1  0
  1 30  1  0
  1 31  1  0
  3 32  1  0
  3 33  1  0
  4 34  1  0
  4 35  1  0
  5 36  1  6
  6 37  1  0
  7 38  1  0
  7 39  1  0
  9 40  1  0
 10 41  1  0
 12 42  1  0
 12 43  1  0
 13 44  1  0
 13 45  1  0
 14 46  1  0
 14 47  1  0
 16 48  1  0
 16 49  1  0
 16 50  1  0
 17 51  1  1
 18 52  1  0
 18 53  1  0
 19 54  1  0
 19 55  1  0
 20 56  1  1
 21 57  1  1
 22 58  1  0
 22 59  1  0
 22 60  1  0
 23 61  1  0
 23 62  1  0
 24 63  1  0
 24 64  1  0
 25 65  1  0
 25 66  1  0
 27 67  1  0
 27 68  1  0
 27 69  1  0
 28 70  1  0
 28 71  1  0
 28 72  1  0
 29 73  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(3beta,5Z,7E)-9,10-Secocholesta-5,7,10(19)-triene-3,25-diol	ChEBI
(3S,5Z,7E)-9,10-Secocholesta-5,7,10-triene-3,25-diol	ChEBI
(5Z,7E)-(3S)-9,10-Secocholesta-5,7,10(19)-triene-3,25-diol	ChEBI
25(OH)D3	ChEBI
25-Hydroxycholecalciferol	ChEBI
25-Hydroxyvitamin D3	ChEBI
3-{2-[1-(5-hydroxy-1,5-dimethyl-hexyl)-7a-methyl-octahydro-inden-4-ylidene]-ethylidene}-4-methylene-cyclohexanol	ChEBI
Calcifediol	ChEBI
Calcifediol anhydrous	ChEBI
Calcifediolum	ChEBI
Rayaldee	ChEBI
(3S,5Z,7E)-9,10-Seco-5,7,10(19)-cholestatriene-3,25-diol	Kegg
(3b,5Z,7E)-9,10-Secocholesta-5,7,10(19)-triene-3,25-diol	Generator
(3Β,5Z,7E)-9,10-secocholesta-5,7,10(19)-triene-3,25-diol	Generator
25-Hydroxy-cholecalciferol	HMDB
5,6-cis-25-Hydroxyvitamin D3	HMDB
9,10-Secocholesta-5,7,10(19)-triene-3b,25-diol	HMDB
Calderol	HMDB
Didrogyl	HMDB
Hidroferol	HMDB
25 Hydroxyvitamin D3	HMDB
Calcifediol, (3 beta,5E,7E)-isomer	HMDB
Monohydrate, 25-hydroxycholecalciferol	HMDB
25-Hydroxycholecalciferol monohydrate	HMDB
Anhydrous, calcifediol	HMDB
Organon brand OF calcifediol	HMDB
25 Hydroxyvitamin D 3	HMDB
25-Hydroxyvitamin D 3	HMDB
Aventis brand OF calcifediol	HMDB
Calcifediol aventis brand	HMDB
Calcifediol organon brand	HMDB
Dedrogyl	HMDB
25 Hydroxycholecalciferol	HMDB
25 Hydroxycholecalciferol monohydrate	HMDB
Calcifediol faes brand	HMDB
Calcifediol, (3 alpha,5Z,7E)-isomer	HMDB
Faes brand OF calcifediol	HMDB
Calcidiol	MeSH

Chemical Formula

C₂₇H₄₄O₂

Average Molecular Weight

400.6371

Monoisotopic Molecular Weight

400.334130652

IUPAC Name

(1S,3Z)-3-{2-[(1R,3aS,4E,7aR)-1-[(2R)-6-hydroxy-6-methylheptan-2-yl]-7a-methyl-octahydro-1H-inden-4-ylidene]ethylidene}-4-methylidenecyclohexan-1-ol

Traditional Name

25-hydroxyvitamin D3

CAS Registry Number

19356-17-3

SMILES

C[C@H](CCCC(C)(C)O)[C@@]1([H])CC[C@@]2([H])\C(CCC[C@]12C)=C\C=C1\C[C@@H](O)CCC1=C

InChI Identifier

InChI=1S/C27H44O2/c1-19-10-13-23(28)18-22(19)12-11-21-9-7-17-27(5)24(14-15-25(21)27)20(2)8-6-16-26(3,4)29/h11-12,20,23-25,28-29H,1,6-10,13-18H2,2-5H3/b21-11+,22-12-/t20-,23+,24-,25+,27-/m1/s1

InChI Key

JWUBBDSIWDLEOM-DTOXIADCSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as vitamin d and derivatives. Vitamin D and derivatives are compounds containing a secosteroid backbone, usually secoergostane or secocholestane.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Vitamin D and derivatives

Direct Parent

Vitamin D and derivatives

Alternative Parents

Substituents

Triterpenoid
Tertiary alcohol
Cyclic alcohol
Secondary alcohol
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

diol (CHEBI:17933 )
D3 vitamins (CHEBI:17933 )
hydroxycalciol (CHEBI:17933 )
Vitamin D3 and derivatives (C01561 )
Vitamin D3 and derivatives (LMST03020246 )

Ontology

Physiological effect

Health effect

Renal system and urinary system

Renal disorder

Chronic kidney disease (HMDB: HMDB0003550)
Nephrotic syndrome (HMDB: HMDB0003550)

Observation

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 227368)

Cellular substructure

Organelle

Mitochondrion (HMDB: HMDB0003550)

Tissue

Epithelium

Epidermis (HMDB: HMDB0003550)

Nervous tissue

Hepatic tissue (HMDB: HMDB0003550)

Organ

Excreta

Biofluid or Excreta

Urine (PMID: 6969729)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0003550)

Source

Exogenous

Exogenous (HMDB: HMDB0003550)

Food

Food (HMDB: HMDB0003550)

Animal origin

Poultry

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Egg

Eggs (FooDB: FOOD00619)

Herb and spice

Herb

Spice

Herb and spice mixture

Curry powder (FooDB: FOOD00678)

Anchovy (FooDB: FOOD00566)
Blue whiting (FooDB: FOOD00567)
Carp bream (FooDB: FOOD00568)
Clupeinae (Herring, Sardine, Sprat) (FooDB: FOOD00520)
Burbot (FooDB: FOOD00313)
Sturgeon (FooDB: FOOD00570)
Charr (FooDB: FOOD00571)
Gadus (Common cod) (FooDB: FOOD00515)
Common dab (FooDB: FOOD00574)
Spiny dogfish (FooDB: FOOD00575)
Anguilliformes (FooDB: FOOD00577)
Flatfish (FooDB: FOOD00535)
Garfish (FooDB: FOOD00579)
Haddock (FooDB: FOOD00374)
Gadiformes (FooDB: FOOD00580)
Atlantic halibut (FooDB: FOOD00516)
Greenland halibut/turbot (FooDB: FOOD00370)
Lake trout (FooDB: FOOD00582)
Lemon sole (FooDB: FOOD00583)
Common ling (FooDB: FOOD00397)
Lumpsucker (FooDB: FOOD00585)
Scombridae (Bonito, Mackerel, Tuna) (FooDB: FOOD00586)
Norway haddock (FooDB: FOOD00588)
Norway pout (FooDB: FOOD00590)
Perciformes (FooDB: FOOD00527)
Northern pike (FooDB: FOOD00431)
Pikeperch (FooDB: FOOD00595)
Pleuronectidae (Dab, Halibut, Plaice) (FooDB: FOOD00596)
Pollock (FooDB: FOOD00513)
Rainbow trout (FooDB: FOOD00444)
Pacific ocean perch (FooDB: FOOD00598)
Salmonidae (Salmon, Trout) (FooDB: FOOD00493)
Catfish (FooDB: FOOD00605)
Thunnus (FooDB: FOOD00607)
Turbot (FooDB: FOOD00364)
Whitefish (FooDB: FOOD00503)
Whiting (FooDB: FOOD00504)
Atlantic wolffish (FooDB: FOOD00296)

Crustacean

Fish product

Other fish product (FooDB: FOOD00665)

Amphibian

True frog (FooDB: FOOD00578)

Mollusk

Pinniped

True seal (FooDB: FOOD00600)

Seaweed

Kombu (FooDB: FOOD00602)
Agar (FooDB: FOOD00284)

Cetacean

Cetacea (Dolphin, Porpoise, Whale) (FooDB: FOOD00609)

Fruit

Pome

Drupe

Apricot (FooDB: FOOD00144)
Prunus (Cherry, Plum) (FooDB: FOOD00143)
Nectarine (FooDB: FOOD00229)
Peach (FooDB: FOOD00149)
European plum (FooDB: FOOD00147)

Berry

Bilberry (FooDB: FOOD00193)
Rubus (Blackberry, Raspberry) (FooDB: FOOD00160)
Vaccinium (Blueberry, Cranberry, Huckleberry) (FooDB: FOOD00188)
Blackcurrant (FooDB: FOOD00155)
Redcurrant (FooDB: FOOD00156)
Elderberry (FooDB: FOOD00358)
Gooseberry (FooDB: FOOD00157)
Grape (FooDB: FOOD00369)
Lingonberry (FooDB: FOOD00194)
Loganberry (FooDB: FOOD00400)
Strawberry (FooDB: FOOD00083)

Tropical fruit

Other fruit

Date (FooDB: FOOD00135)
Fig (FooDB: FOOD00081)

Fruit product

Other fruit product (FooDB: FOOD00765)
Fruit preserve (FooDB: FOOD00660)

Citrus

Grapefruit (FooDB: FOOD00256)
Lemon (FooDB: FOOD00054)
Lime (FooDB: FOOD00053)
Sweet orange (FooDB: FOOD00057)
Mandarin orange (Clementine, Tangerine) (FooDB: FOOD00056)

Beverage

Distilled beverage

Spirit (FooDB: FOOD00276)
Liquor (FooDB: FOOD00616)
Whisky (FooDB: FOOD00623)

Fermented beverage

Beer (FooDB: FOOD00268)
Grape wine (FooDB: FOOD00612)

Other beverage

Fortified wines

Sherry (FooDB: FOOD00632)
Vermouth (FooDB: FOOD00631)

Water

Water (FooDB: FOOD00664)

Alcoholic beverage

Other alcoholic beverage (FooDB: FOOD00278)

Onion-family vegetable

Leek (FooDB: FOOD00007)
Allium (FooDB: FOOD00005)

Other vegetable

Okra (FooDB: FOOD00420)

Stalk vegetable

Garden rhubarb (FooDB: FOOD00154)

Baby food

Baby food (FooDB: FOOD00668)

Cereal and cereal product

Other bread

Other bread (FooDB: FOOD00269)

Leavened bread

Wheat bread (FooDB: FOOD00808)
Rye bread (FooDB: FOOD00809)

Cereal

Barley (FooDB: FOOD00088)
Common buckwheat (FooDB: FOOD00079)
Corn (FooDB: FOOD00205)
Millet (FooDB: FOOD00126)
Oat (FooDB: FOOD00022)
Rice (FooDB: FOOD00125)
Rye (FooDB: FOOD00169)
Wheat (FooDB: FOOD00561)
Hard wheat (FooDB: FOOD00242)
White bread (FooDB: FOOD00987)

Cereal product

Bread products

Other bread product (FooDB: FOOD00805)

Flat bread

Crisp bread (FooDB: FOOD00640)

Baking good

Sugar

Sugar (FooDB: FOOD00651)

Dressing

Salad dressing (FooDB: FOOD00645)

Condiment

Substitute

Sugar substitute (FooDB: FOOD00656)

Seasoning

Salt (FooDB: FOOD00647)

Sauce

Sauce (FooDB: FOOD00646)

Pulse

Bean

Lentil

Lentils (FooDB: FOOD00098)

Pea

Chickpea (FooDB: FOOD00047)
Common pea (FooDB: FOOD00141)

Soy

Soy bean (FooDB: FOOD00085)

Soy product

Miso (FooDB: FOOD00695)
Soy milk (FooDB: FOOD00736)
Soy sauce (FooDB: FOOD00694)
Tofu (FooDB: FOOD00696)

Unclassified food or beverage

Unclassified food or beverage (FooDB: FOOD00672)

Dish

Ground meat

Sausage (FooDB: FOOD00652)
Meatball (FooDB: FOOD00653)
Pate (FooDB: FOOD00655)
Cold cut (FooDB: FOOD00770)

Other dish

Dumpling (FooDB: FOOD00669)
Other dish (FooDB: FOOD00836)
Pizza (FooDB: FOOD00637)
Soup (FooDB: FOOD00670)

Fat and oil

Vegetable fat

Margarine-like spread (FooDB: FOOD00844)
Margarine (FooDB: FOOD00843)

Animal fat

Fish oil (FooDB: FOOD00990)

Milk and milk product

Other milk product

Butter (FooDB: FOOD00648)
Casein (FooDB: FOOD00659)
Whey (FooDB: FOOD00658)
Cream (FooDB: FOOD00650)
Dried milk (FooDB: FOOD00689)

Fermented milk product

Cheese (FooDB: FOOD00617)
Yogurt (FooDB: FOOD00620)
Ymer (FooDB: FOOD00638)

Pastry (FooDB: FOOD00641)
Gelatin dessert (FooDB: FOOD00725)

Frozen dessert

Ice cream (FooDB: FOOD00624)
Other frozen dessert (FooDB: FOOD00729)

Other confectionery

Spread

Chocolate spread (FooDB: FOOD00676)

Cocoa and cocoa product

Cocoa product

Coffee and coffee product

Coffee

Snack

Cracker (FooDB: FOOD00787)
Other snack food (FooDB: FOOD00639)

Tea

Endogenous

Endogenous (HMDB: HMDB0003550)

Signaling molecule (HMDB: HMDB0003550)

Industrial application

Bone density conservation agent (HMDB: HMDB0003550)
Nutraceutical (HMDB: HMDB0003550)

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0003550)

Food and nutrition

Nutritional supplement (HMDB: HMDB0003550)

Pharmaceutical industry

Pharmaceutical (HMDB: HMDB0003550)

Biomarker

Nephrotic syndrome (MarkerDB: MDB00000426)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M-H]-	Not Available	200.064	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000269

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.0022 g/L	ALOGPS
logP	6.71	ALOGPS
logP	5.65	ChemAxon
logS	-5.3	ALOGPS
pKa (Strongest Acidic)	18.38	ChemAxon
pKa (Strongest Basic)	-0.98	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	40.46 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	125.06 m³·mol⁻¹	ChemAxon
Polarizability	50.32 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	197.668	31661259
DarkChem	[M-H]-	195.308	31661259
DeepCCS	[M-2H]-	236.923	30932474
DeepCCS	[M+Na]+	211.542	30932474
AllCCS	[M+H]+	205.9	32859911
AllCCS	[M+H-H2O]+	203.7	32859911
AllCCS	[M+NH4]+	207.9	32859911
AllCCS	[M+Na]+	208.4	32859911
AllCCS	[M-H]-	205.2	32859911
AllCCS	[M+Na-2H]-	207.1	32859911
AllCCS	[M+HCOO]-	209.5	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
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.	9.22 minutes	32390414
Predicted by Siyang on May 30, 2022	25.2193 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.41 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	3487.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	702.8 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	292.4 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	280.2 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	611.6 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	1205.8 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	1099.7 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	98.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	2089.5 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	661.0 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	2061.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	810.3 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	575.7 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	402.6 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	781.1 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	8.9 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Calcidiol	C[C@H](CCCC(C)(C)O)[C@@]1([H])CC[C@@]2([H])\C(CCC[C@]12C)=C\C=C1\C[C@@H](O)CCC1=C	3361.7	Standard polar	33892256
Calcidiol	C[C@H](CCCC(C)(C)O)[C@@]1([H])CC[C@@]2([H])\C(CCC[C@]12C)=C\C=C1\C[C@@H](O)CCC1=C	3265.4	Standard non polar	33892256
Calcidiol	C[C@H](CCCC(C)(C)O)[C@@]1([H])CC[C@@]2([H])\C(CCC[C@]12C)=C\C=C1\C[C@@H](O)CCC1=C	3362.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Calcidiol,1TMS,isomer #1	C=C1CC[C@H](O)C/C1=C/C=C1\CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CCCC(C)(C)O[Si](C)(C)C	3382.8	Semi standard non polar	33892256
Calcidiol,1TMS,isomer #2	C=C1CC[C@H](O[Si](C)(C)C)C/C1=C/C=C1\CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CCCC(C)(C)O	3266.7	Semi standard non polar	33892256
Calcidiol,2TMS,isomer #1	C=C1CC[C@H](O[Si](C)(C)C)C/C1=C/C=C1\CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CCCC(C)(C)O[Si](C)(C)C	3361.3	Semi standard non polar	33892256
Calcidiol,1TBDMS,isomer #1	C=C1CC[C@H](O)C/C1=C/C=C1\CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CCCC(C)(C)O[Si](C)(C)C(C)(C)C	3612.5	Semi standard non polar	33892256
Calcidiol,1TBDMS,isomer #2	C=C1CC[C@H](O[Si](C)(C)C(C)(C)C)C/C1=C/C=C1\CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CCCC(C)(C)O	3467.1	Semi standard non polar	33892256
Calcidiol,2TBDMS,isomer #1	C=C1CC[C@H](O[Si](C)(C)C(C)(C)C)C/C1=C/C=C1\CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CCCC(C)(C)O[Si](C)(C)C(C)(C)C	3829.2	Semi standard non polar	33892256

Spectra

Biological Properties

Cellular Locations

Cytoplasm
Extracellular
Membrane (predicted from logP)
Mitochondria

Biospecimen Locations

Blood
Urine

Tissue Locations

Epidermis
Kidney
Ovary
Prostate
Testis

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	0.0600 +/- 0.0222 uM	Adult (>18 years old)	Female	Normal	22523182	details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	32966057	details
Blood	Detected and Quantified	>0.0749 uM	Not Specified	Not Specified	Normal	26537508	details
Blood	Detected and Quantified	0.0300-0.155 uM	Not Specified	Not Specified	Normal	23430506	details
Blood	Detected and Quantified	0.0830 +/- 0.0320 uM	Adult (>18 years old)	Male	Normal	8424386	details
Blood	Detected and Quantified	0.0790 +/- 0.0340 uM	Adult (>18 years old)	Male	Normal	8424386	details
Blood	Detected and Quantified	0.108 uM	Adult (>18 years old)	Male	Normal	9109609	details
Blood	Detected and Quantified	0.095 uM	Adult (>18 years old)	Male	Normal	9109609	details
Blood	Detected and Quantified	0.0730 +/- 0.0310 uM	Adult (>18 years old)	Female	Normal	8424386	details
Blood	Detected and Quantified	0.0700 +/- 0.0310 uM	Adult (>18 years old)	Female	Normal	8424386	details
Blood	Detected and Quantified	0.0831 uM	Adult (>18 years old)	Female	Normal	20332276	details
Blood	Detected and Quantified	0.078 uM	Adult (>18 years old)	Female	Normal	9109609	details
Blood	Detected and Quantified	0.07 uM	Adult (>18 years old)	Female	Normal	9109609	details
Blood	Detected and Quantified	0.0600 +/- 0.0146 uM	Adult (>18 years old)	Both	Normal	20332255	details
Blood	Detected and Quantified	0.0469 uM	Adult (>18 years old)	Both	Normal	22975199	details
Blood	Detected and Quantified	0.0678 +/- 0.0222 uM	Adult (>18 years old)	Female	Normal	22523182	details
Blood	Detected and Quantified	0.0547 uM	Adult (>18 years old)	Female	Normal	8279408	details
Blood	Detected and Quantified	0.13 (0.13-0.14) uM	Adult (>18 years old)	Both	Normal	227368	details
Blood	Detected and Quantified	0.0245 +/- 0.023 uM	Adult (>18 years old)	Both	Normal	Geigy Scientific ...	details
Blood	Detected and Quantified	0.0422 uM	Adult (>18 years old)	Both	Normal	22975199	details
Blood	Detected and Quantified	0.035 uM	Adult (>18 years old)	Female	Normal	8279408	details
Blood	Detected and Quantified	0.042 uM	Adult (>18 years old)	Female	Normal	8279408	details
Blood	Detected and Quantified	0.044 uM	Adult (>18 years old)	Female	Normal	8279408	details
Blood	Detected and Quantified	0.0689 (0.0459-0.0919) uM	Adult (>18 years old)	Both	Normal	227368	details
Blood	Detected and Quantified	0.057 uM	Adult (>18 years old)	Female	Normal	8279408	details
Blood	Detected and Quantified	0.0634 uM	Adult (>18 years old)	Female	Normal	8279408	details
Blood	Detected and Quantified	0.064 uM	Adult (>18 years old)	Female	Normal	8279408	details
Blood	Detected and Quantified	0.074 uM	Adult (>18 years old)	Female	Normal	8279408	details
Blood	Detected and Quantified	0.08 uM	Adult (>18 years old)	Female	Normal	8279408	details
Blood	Detected and Quantified	0.081 uM	Adult (>18 years old)	Female	Normal	8279408	details
Blood	Detected and Quantified	0.0577 uM	Adult (>18 years old)	Both	Normal	22975199	details
Urine	Detected and Quantified	0.092 +/- 0.0037 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	6969729	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	32966057	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	0.044 (0.013-0.074) uM	Adult (>18 years old)	Both	Anephrism	227368	details
Blood	Detected and Quantified	0.0137 uM	Infant (0-1 year old)	Female	Pyroglutamic aciduria	23430506	details
Blood	Detected and Quantified	0.0549 +/- 0.0225 uM	Children (1-13 years old)	Both	Adrenal hyperplasia, congenital, due to 3-beta-hydroxysteroid dehydrogenase 2 deficiency	26079780	details
Blood	Detected and Quantified	0.0449 +/- 0.00749 uM	Children (1-13 years old)	Both	Adrenal hyperplasia, congenital, due to 3-beta-hydroxysteroid dehydrogenase 2 deficiency	26079780	details
Blood	Detected and Quantified	0.0599 +/- 0.0200 uM	Children (1-13 years old)	Both	Adrenal hyperplasia, congenital, due to 3-beta-hydroxysteroid dehydrogenase 2 deficiency	26079780	details
Blood	Detected and Quantified	0.0704 uM	Adult (>18 years old)	Male	Bartter Syndrome, Type 4A, Neonatal, with Sensorineural Deafness	26537508	details
Urine	Detected and Quantified	0.0099 +/- 0.0019 umol/mmol creatinine	Adult (>18 years old)	Both	Nephrotic syndrome	6969729	details

Associated Disorders and Diseases

Disease References

Anephric patients
Shepard RM, Horst RL, Hamstra AJ, DeLuca HF: Determination of vitamin D and its metabolites in plasma from normal and anephric man. Biochem J. 1979 Jul 15;182(1):55-69. [PubMed:227368 ]
Adrenal hyperplasia, congenital, due to 3-beta-hydroxysteroid dehydrogenase 2 deficiency
Benkert AR, Young M, Robinson D, Hendrickson C, Lee PA, Strauss KA: Severe Salt-Losing 3beta-Hydroxysteroid Dehydrogenase Deficiency: Treatment and Outcomes of HSD3B2 c.35G>A Homozygotes. J Clin Endocrinol Metab. 2015 Aug;100(8):E1105-15. doi: 10.1210/jc.2015-2098. Epub 2015 Jun 16. [PubMed:26079780 ]
Bartter Syndrome, Type 4A, Neonatal, with Sensorineural Deafness
Heilberg IP, Totoli C, Calado JT: Adult presentation of Bartter syndrome type IV with erythrocytosis. Einstein (Sao Paulo). 2015 Oct-Dec;13(4):604-6. doi: 10.1590/S1679-45082015RC3013. Epub 2015 Oct 30. [PubMed:26537508 ]
Nephrotic syndrome
Goldstein DA, Haldimann B, Sherman D, Norman AW, Massry SG: Vitamin D metabolites and calcium metabolism in patients with nephrotic syndrome and normal renal function. J Clin Endocrinol Metab. 1981 Jan;52(1):116-21. [PubMed:6969729 ]

Associated OMIM IDs

201810 (Adrenal hyperplasia, congenital, due to 3-beta-hydroxysteroid dehydrogenase 2 deficiency)
602522 (Bartter Syndrome, Type 4A, Neonatal, with Sensorineural Deafness)

External Links

DrugBank ID

DB00146

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

17933

Food Biomarker Ontology

Not Available

VMH ID

25HVITD3

MarkerDB ID

MDB00000426

Good Scents ID

Not Available

References

Synthesis Reference

Mascarenas, J. L.; Mourino, A.; Castedo, L. Studies on the synthesis of side-chain hydroxylated metabolites of vitamin D. 3. Synthesis of 25-ketovitamin D3 and 25-hydroxyvitamin D3. Journal of Organic Chemistry (1986), 51(8), 1269-72.

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Flanagan JN, Young MV, Persons KS, Wang L, Mathieu JS, Whitlatch LW, Holick MF, Chen TC: Vitamin D metabolism in human prostate cells: implications for prostate cancer chemoprevention by vitamin D. Anticancer Res. 2006 Jul-Aug;26(4A):2567-72. [PubMed:16886665 ]
Shepard RM, Horst RL, Hamstra AJ, DeLuca HF: Determination of vitamin D and its metabolites in plasma from normal and anephric man. Biochem J. 1979 Jul 15;182(1):55-69. [PubMed:227368 ]
Passadakis P, Ersoy F, Tam P, Memmos D, Siamopoulos K, Ozener C, Akcicek F, Camsari T, Ates K, Ataman R, Vlachojannis J, Dombros N, Utas C, Akpolat T, Bozfakioglu S, Wu GG, Karayaylali I, Arinsoy T, Stathakis C, Yavuz M, Tsakiris D, Dimitriades A, Yilmaz ME, Gultekin M, Karayalcin B, Challa A, Polat N, Oreopoulos DG: Serum levels of prostate-specific antigen and vitamin D in peritoneal dialysis patients. Adv Perit Dial. 2004;20:203-8. [PubMed:15384827 ]
Park SB, Suh DH, Youn JI: A pilot study to assess the safety and efficacy of topical calcipotriol treatment in childhood psoriasis. Pediatr Dermatol. 1999 Jul-Aug;16(4):321-5. [PubMed:10469423 ]
Haden ST, Fuleihan GE, Angell JE, Cotran NM, LeBoff MS: Calcidiol and PTH levels in women attending an osteoporosis program. Calcif Tissue Int. 1999 Apr;64(4):275-9. [PubMed:10089217 ]
Gacad MA, Adams JS: Proteins in the heat shock-70 family specifically bind 25-hydroxyvitamin D3 and 17beta-estradiol. J Clin Endocrinol Metab. 1998 Apr;83(4):1264-7. [PubMed:9543154 ]
Feingold KR, Williams ML, Pillai S, Menon GK, Halloran BP, Bikle DD, Elias PM: The effect of vitamin D status on cutaneous sterologenesis in vivo and in vitro. Biochim Biophys Acta. 1987 Sep 14;930(2):193-200. [PubMed:3040120 ]
DeLuca HF: Overview of general physiologic features and functions of vitamin D. Am J Clin Nutr. 2004 Dec;80(6 Suppl):1689S-96S. [PubMed:15585789 ]
Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Drager A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlic A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO: Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. 2018 Mar;36(3):272-281. doi: 10.1038/nbt.4072. Epub 2018 Feb 19. [PubMed:29457794 ]

Enzymes

Enzyme Details

1. 25-hydroxyvitamin D-1 alpha hydroxylase, mitochondrial

General function:: Involved in monooxygenase activity
Specific function:: Catalyzes the conversion of 25-hydroxyvitamin D3 (25(OH)D) to 1-alpha,25-dihydroxyvitamin D3 (1,25(OH)2D) plays an important role in normal bone growth, calcium metabolism, and tissue differentiation.
Gene Name:: CYP27B1
Uniprot ID:: O15528
Molecular weight:: 56503.475

Reactions

Calcidiol + NADPH + Oxygen → Calcitriol + NADP + Water	details
Calcidiol + Oxygen + NADPH + Hydrogen Ion → Calcitriol + NADP + Water	details

References

Schuster I: Cytochromes P450 are essential players in the vitamin D signaling system. Biochim Biophys Acta. 2011 Jan;1814(1):186-99. doi: 10.1016/j.bbapap.2010.06.022. Epub 2010 Jul 7. [PubMed:20619365 ]
Bernad M, Jaramillo G, Aguado P, del Campo T, Coya J, Martin Mola E, Gijon Banos J, Saldana Barrera H, Martinez ME: [Polymorphism of the gene of vitamin D receptor and bone mineral density in postmenopausal women]. Med Clin (Barc). 1999 May 15;112(17):651-5. [PubMed:10374186 ]
Diesel B, Radermacher J, Bureik M, Bernhardt R, Seifert M, Reichrath J, Fischer U, Meese E: Vitamin D(3) metabolism in human glioblastoma multiforme: functionality of CYP27B1 splice variants, metabolism of calcidiol, and effect of calcitriol. Clin Cancer Res. 2005 Aug 1;11(15):5370-80. [PubMed:16061850 ]
Eto TA, Nakamura Y, Taniguchi T, Miyamoto K, Nagatomo J, Maeda Y, Higashi S, Okuda K, Setoguchi T: Assay of 25-hydroxyvitamin D3 1 alpha-hydroxylase in rat kidney mitochondria. Anal Biochem. 1998 Apr 10;258(1):53-8. [PubMed:9527847 ]
Hart GR, Furniss JL, Laurie D, Durham SK: Measurement of vitamin D status: background, clinical use, and methodologies. Clin Lab. 2006;52(7-8):335-43. [PubMed:16955631 ]
Vigo Gago E, Cadarso-Suarez C, Perez-Fernandez R, Romero Burgos R, Devesa Mugica J, Segura Iglesias C: Association between vitamin D receptor FokI. Polymorphism and serum parathyroid hormone level in patients with chronic renal failure. J Endocrinol Invest. 2005 Feb;28(2):117-21. [PubMed:15887856 ]

Enzyme Details

2. Vitamin D3 receptor

General function:: Involved in sequence-specific DNA binding transcription factor activity
Specific function:: Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis
Gene Name:: VDR
Uniprot ID:: P11473
Molecular weight:: 48288.6

References

Reinhart GA: Vitamin D analogs: novel therapeutic agents for cardiovascular disease? Curr Opin Investig Drugs. 2004 Sep;5(9):947-51. [PubMed:15503649 ]
Chen X, Ji ZL, Chen YZ: TTD: Therapeutic Target Database. Nucleic Acids Res. 2002 Jan 1;30(1):412-5. [PubMed:11752352 ]

Enzyme Details

3. 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial

General function:: Involved in monooxygenase activity
Specific function:: Has a role in maintaining calcium homeostasis. Catalyzes the NADPH-dependent 24-hydroxylation of calcidiol (25-hydroxyvitamin D(3)) and calcitriol (1-alpha,25-dihydroxyvitamin D(3)). The enzyme can perform up to 6 rounds of hydroxylation of calcitriol leading to calcitroic acid. It also shows 23-hydroxylating activity leading to 1-alpha,25-dihydroxyvitamin D(3)-26,23-lactone as end product.
Gene Name:: CYP24A1
Uniprot ID:: Q07973
Molecular weight:: 58874.695

Reactions

Calcidiol + NADPH + Oxygen → (24R)-24,25-Dihydroxycalciol + NADP + Water	details
Calcidiol + NADPH + Hydrogen Ion + Oxygen → Secalciferol + NADP + Water	details

References

Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. doi: 10.1093/nar/gkp970. Epub 2009 Nov 24. [PubMed:19934256 ]

Enzyme Details

4. Vitamin D 25-hydroxylase

General function:: Involved in monooxygenase activity
Specific function:: Has a D-25-hydroxylase activity on both forms of vitamin D, vitamin D(2) and D(3).
Gene Name:: CYP2R1
Uniprot ID:: Q6VVX0
Molecular weight:: 57358.82

Reactions

Vitamin D3 + Oxygen + NADPH → Calcidiol + NADP(+) H(2)O	details
Calcidiol + NADP + Water → Vitamin D3 + NADPH + Hydrogen Ion + Oxygen	details

Showing metabocard for Calcidiol (HMDB0003550)

MOL for HMDB0003550 (Calcidiol)

3D MOL for HMDB0003550 (Calcidiol)

3D SDF for HMDB0003550 (Calcidiol)

3D-SDF for HMDB0003550 (Calcidiol)

PDB for HMDB0003550 (Calcidiol)

3D PDB for HMDB0003550 (Calcidiol)

SMILES for HMDB0003550 (Calcidiol)

INCHI for HMDB0003550 (Calcidiol)

Structure for HMDB0003550 (Calcidiol)

3D Structure for HMDB0003550 (Calcidiol)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

Enzymes

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References

References

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References

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