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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (2) Show 2 proteins XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2009-07-13 12:02:10 UTC

Update Date

2022-03-07 02:51:26 UTC

HMDB ID

HMDB0012453

Secondary Accession Numbers

HMDB12453

Metabolite Identification

Common Name

3beta-Hydroxy-5-cholestenoic acid

Description

3beta-Hydroxy-5-cholestenoic acid (CAS: 6561-58-6) belongs to the class of organic compounds known as monohydroxy bile acids, alcohols, and derivatives. These are bile acids, alcohols or any of their derivatives bearing a hydroxyl group. 3beta-Hydroxy-5-cholestenoic acid is found in the primary bile acid biosynthesis pathway. 3beta-Hydroxy-5-cholestenoic acid is created from cholest-5-ene-3 beta,26-diol through the action of CYP27A (EC 1.14.13.15). 3beta-Hydroxy-5-cholestenoic acid is then converted into 3beta,7alpha-dihydroxy-5-cholestenoic acid by the action of CYP7B (EC 1.14.13.100). 3beta-Hydroxy-5-cholestenoic acid was identified as one of forty plasma metabolites that could be used to predict gut microbiome Shannon diversity (PMID: 31477923 ). Shannon diversity is a metric that summarizes both species abundance and evenness, and it has been suggested as a marker for microbiome health.

Structure

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


  Mrv1652304062012582D          

 34 37  0  0  0  0            999 V2000
 9998.7140 9999.9320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.5816 9998.6852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9994.4451 9996.6224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2922 9997.4538    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
 9998.0031 9998.6852    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
 9998.7140 9997.4538    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
 9995.8694 9998.2724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.1550 9997.8600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.1550 9997.0350    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9995.8694 9996.6226    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.0039 9999.5160    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2896 9999.1035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2896 9998.2785    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9998.0039 9997.8661    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9996.5787 9997.8600    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9996.5787 9997.0350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2931 9996.6226    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.0075 9997.0350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.7185 9999.1034    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9998.7184 9998.2785    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.5031 9998.0235    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.9879 9998.6911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.5031 9999.3586    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9999.503110000.1836    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.218810000.5961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.932610000.1836    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.648310000.5961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.361910000.1836    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10003.077710000.5961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.793410000.1836    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.077710001.4211    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.3619 9999.3586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.789110000.5961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.2188 9999.7710    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
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  9  3  1  1  0  0  0
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 15  2  1  1  0  0  0
 13 15  1  0  0  0  0
 13  4  1  6  0  0  0
 18 14  1  0  0  0  0
 14  5  1  1  0  0  0
 19 20  1  0  0  0  0
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 23 34  1  6  0  0  0
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 23 19  1  0  0  0  0
 23 22  1  0  0  0  0
 14 20  1  0  0  0  0
 20  6  1  6  0  0  0
 11 19  1  0  0  0  0
 19  1  1  1  0  0  0
M  END

HMDB0012453
     RDKit          3D
3beta-Hydroxy-5-cholestenoic acid
 74 77  0  0  0  0  0  0  0  0999 V2000
   -7.8493    1.9046    0.1077 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2607    0.4916   -0.0717 C   0  0  2  0  0  0  0  0  0  0  0  0
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    4.8906    1.6564    0.3851 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0813    0.5574   -0.2717 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8096    1.0307   -1.7053 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.2256    2.4309   -0.3315 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1652304062012582D          

 34 37  0  0  0  0            999 V2000
 9998.7140 9999.9320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.5816 9998.6852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9994.4451 9996.6224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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 9998.0039 9999.5160    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 9998.789110000.5961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.2188 9999.7710    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
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 23 22  1  0  0  0  0
 14 20  1  0  0  0  0
 20  6  1  6  0  0  0
 11 19  1  0  0  0  0
 19  1  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0012453

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@]1(CC[C@@]2([H])[C@]3([H])CC=C4C[C@@H](O)CC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCC[C@@H](C)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C27H44O3/c1-17(6-5-7-18(2)25(29)30)22-10-11-23-21-9-8-19-16-20(28)12-14-26(19,3)24(21)13-15-27(22,23)4/h8,17-18,20-24,28H,5-7,9-16H2,1-4H3,(H,29,30)/t17-,18-,20+,21+,22-,23+,24+,26+,27-/m1/s1

> <INCHI_KEY>
WVXOMPRLWLXFAP-KQOPCUSDSA-N

> <FORMULA>
C27H44O3

> <MOLECULAR_WEIGHT>
416.646

> <EXACT_MASS>
416.329045277

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
51.552377269474334

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,6R)-6-[(1S,2R,5S,10S,11S,14R,15R)-5-hydroxy-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-7-en-14-yl]-2-methylheptanoic acid

> <ALOGPS_LOGP>
5.57

> <JCHEM_LOGP>
6.048614447666667

> <ALOGPS_LOGS>
-5.93

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
18.20428950550382

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.8289209924155

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3972440282926124

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
122.30779999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.85e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,6R)-6-[(1S,2R,5S,10S,11S,14R,15R)-5-hydroxy-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-7-en-14-yl]-2-methylheptanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0012453
     RDKit          3D
3beta-Hydroxy-5-cholestenoic acid
 74 77  0  0  0  0  0  0  0  0999 V2000
   -7.8493    1.9046    0.1077 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2607    0.4916   -0.0717 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.8061    0.5336    0.4087 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1247   -0.7663    0.2975 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7593   -0.8886    0.7940 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6421   -0.0716    0.3201 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7169    1.3890    0.5742 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3349   -0.6400    0.8499 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2733   -2.0988    0.3570 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1475   -2.4152    0.0508 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8782   -1.1867    0.5271 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2395   -1.0447   -0.0324 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1220   -2.0832    0.6276 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5106   -1.8588    0.1400 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9300   -0.6652   -0.2621 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3357   -0.5478   -0.7308 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0445    0.3662    0.2616 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.9194    1.1817   -0.4219 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0798    1.1120    1.1346 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8906    1.6564    0.3851 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0813    0.5574   -0.2717 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8096    1.0307   -1.7053 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7767    0.3160    0.4133 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8234    1.4068    0.0664 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4258    1.1864    0.6678 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1066   -0.0974    0.1520 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3175   -0.0911   -1.3438 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4274    0.1211   -1.4675 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9022    0.9754   -2.2925 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1213   -1.1026   -2.0463 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4071    2.4160    0.9661 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9421    1.7885    0.1793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6471    2.4418   -0.8399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8873   -0.1690    0.5599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8187    0.9271    1.4289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3710    1.3298   -0.2542 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2678   -1.2430   -0.7278 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7592   -1.4875    0.9256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4449   -1.9845    0.7032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8196   -0.7915    1.9362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5723   -0.1948   -0.8100 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6460    1.7889    0.9963 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4654    1.9960   -0.3087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9861    1.5769    1.4445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2823   -0.5496    1.9291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6512   -2.7479    1.1960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8790   -2.2647   -0.5470 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4480   -3.3248    0.6442 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3755   -2.6664   -0.9943 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9454   -1.2585    1.6319 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3250   -1.1835   -1.1135 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7766   -3.1171    0.4458 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1247   -1.8273    1.7233 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1895   -2.7201    0.1215 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8090   -1.5315   -0.8105 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3809   -0.0982   -1.7562 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6236   -0.3242    0.9320 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7977    0.7241   -0.4615 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7230    0.5286    1.9946 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6231    1.9888    1.5506 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2405    2.1561    1.1187 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2256    2.4309   -0.3315 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5265    2.1184   -1.6213 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7631    1.0302   -2.2719 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0321    0.4187   -2.1624 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8882    0.2890    1.5109 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2458    2.3599    0.4465 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6644    1.5485   -1.0149 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1252    2.0858    0.2926 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5365    1.1530    1.7533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9620    0.7266   -1.6561 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7037   -1.0812   -1.6389 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6631    0.0042   -1.8882 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6621   -1.9334   -1.7896 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  6
 21 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  1  6
  2 28  1  0
 28 29  2  0
 28 30  1  0
 26  8  1  0
 26 11  1  0
 23 12  1  0
 21 15  1  0
  1 31  1  0
  1 32  1  0
  1 33  1  0
  2 34  1  1
  3 35  1  0
  3 36  1  0
  4 37  1  0
  4 38  1  0
  5 39  1  0
  5 40  1  0
  6 41  1  6
  7 42  1  0
  7 43  1  0
  7 44  1  0
  8 45  1  1
  9 46  1  0
  9 47  1  0
 10 48  1  0
 10 49  1  0
 11 50  1  1
 12 51  1  6
 13 52  1  0
 13 53  1  0
 14 54  1  0
 16 55  1  0
 16 56  1  0
 17 57  1  1
 18 58  1  0
 19 59  1  0
 19 60  1  0
 20 61  1  0
 20 62  1  0
 22 63  1  0
 22 64  1  0
 22 65  1  0
 23 66  1  1
 24 67  1  0
 24 68  1  0
 25 69  1  0
 25 70  1  0
 27 71  1  0
 27 72  1  0
 27 73  1  0
 30 74  1  0
M  END

HEADER    PROTEIN                                 06-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-APR-20         0                                  
HETATM    1  C   UNK     0    8664.2668666.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8660.2868664.212   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0    8656.2988660.362   0.000  0.00  0.00           O+0
HETATM    4  H   UNK     0    8661.6128661.914   0.000  0.00  0.00           H+0
HETATM    5  H   UNK     0    8662.9398664.212   0.000  0.00  0.00           H+0
HETATM    6  H   UNK     0    8664.2668661.914   0.000  0.00  0.00           H+0
HETATM    7  C   UNK     0    8658.9568663.442   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8657.6238662.672   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8657.6238661.132   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8658.9568660.362   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8662.9418665.763   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8661.6078664.993   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8661.6078663.453   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8662.9418662.683   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8660.2808662.672   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8660.2808661.132   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8661.6148660.362   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8662.9478661.132   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0    8664.2758664.993   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0    8664.2748663.453   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0    8665.7398662.977   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0    8666.6448664.223   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0    8665.7398665.469   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0    8665.7398667.009   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0    8667.0758667.779   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0    8668.4088667.009   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0    8669.7438667.779   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0    8671.0768667.009   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0    8672.4128667.779   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0    8673.7488667.009   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0    8672.4128669.319   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0    8671.0768665.469   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0    8664.4068667.779   0.000  0.00  0.00           C+0
HETATM   34  H   UNK     0    8667.0758666.239   0.000  0.00  0.00           H+0
CONECT    1   19                                                            
CONECT    2   15                                                            
CONECT    3    9                                                            
CONECT    4   13                                                            
CONECT    5   14                                                            
CONECT    6   20                                                            
CONECT    7    8   15                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10    3                                                  
CONECT   10    9   16                                                       
CONECT   11   12   19                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15    4                                             
CONECT   14   13   18    5   20                                             
CONECT   15   16    7    2   13                                             
CONECT   16   15   17   10                                                  
CONECT   17   16   18                                                       
CONECT   18   17   14                                                       
CONECT   19   20   23   11    1                                             
CONECT   20   19   21   14    6                                             
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   24   34   19   22                                             
CONECT   24   23   25   33                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   32                                                  
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29                                                            
CONECT   32   28                                                            
CONECT   33   24                                                            
CONECT   34   23                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   74    0
END

COMPND    HMDB0012453
HETATM    1  C1  UNL     1      -7.849   1.905   0.108  1.00  0.00           C  
HETATM    2  C2  UNL     1      -7.261   0.492  -0.072  1.00  0.00           C  
HETATM    3  C3  UNL     1      -5.806   0.534   0.409  1.00  0.00           C  
HETATM    4  C4  UNL     1      -5.125  -0.766   0.297  1.00  0.00           C  
HETATM    5  C5  UNL     1      -3.759  -0.889   0.794  1.00  0.00           C  
HETATM    6  C6  UNL     1      -2.642  -0.072   0.320  1.00  0.00           C  
HETATM    7  C7  UNL     1      -2.717   1.389   0.574  1.00  0.00           C  
HETATM    8  C8  UNL     1      -1.335  -0.640   0.850  1.00  0.00           C  
HETATM    9  C9  UNL     1      -1.273  -2.099   0.357  1.00  0.00           C  
HETATM   10  C10 UNL     1       0.147  -2.415   0.051  1.00  0.00           C  
HETATM   11  C11 UNL     1       0.878  -1.187   0.527  1.00  0.00           C  
HETATM   12  C12 UNL     1       2.240  -1.045  -0.032  1.00  0.00           C  
HETATM   13  C13 UNL     1       3.122  -2.083   0.628  1.00  0.00           C  
HETATM   14  C14 UNL     1       4.511  -1.859   0.140  1.00  0.00           C  
HETATM   15  C15 UNL     1       4.930  -0.665  -0.262  1.00  0.00           C  
HETATM   16  C16 UNL     1       6.336  -0.548  -0.731  1.00  0.00           C  
HETATM   17  C17 UNL     1       7.044   0.366   0.262  1.00  0.00           C  
HETATM   18  O1  UNL     1       7.919   1.182  -0.422  1.00  0.00           O  
HETATM   19  C18 UNL     1       6.080   1.112   1.135  1.00  0.00           C  
HETATM   20  C19 UNL     1       4.891   1.656   0.385  1.00  0.00           C  
HETATM   21  C20 UNL     1       4.081   0.557  -0.272  1.00  0.00           C  
HETATM   22  C21 UNL     1       3.810   1.031  -1.705  1.00  0.00           C  
HETATM   23  C22 UNL     1       2.777   0.316   0.413  1.00  0.00           C  
HETATM   24  C23 UNL     1       1.823   1.407   0.066  1.00  0.00           C  
HETATM   25  C24 UNL     1       0.426   1.186   0.668  1.00  0.00           C  
HETATM   26  C25 UNL     1      -0.107  -0.097   0.152  1.00  0.00           C  
HETATM   27  C26 UNL     1      -0.318  -0.091  -1.344  1.00  0.00           C  
HETATM   28  C27 UNL     1      -7.427   0.121  -1.467  1.00  0.00           C  
HETATM   29  O2  UNL     1      -7.902   0.975  -2.292  1.00  0.00           O  
HETATM   30  O3  UNL     1      -7.121  -1.103  -2.046  1.00  0.00           O  
HETATM   31  H1  UNL     1      -7.407   2.416   0.966  1.00  0.00           H  
HETATM   32  H2  UNL     1      -8.942   1.788   0.179  1.00  0.00           H  
HETATM   33  H3  UNL     1      -7.647   2.442  -0.840  1.00  0.00           H  
HETATM   34  H4  UNL     1      -7.887  -0.169   0.560  1.00  0.00           H  
HETATM   35  H5  UNL     1      -5.819   0.927   1.429  1.00  0.00           H  
HETATM   36  H6  UNL     1      -5.371   1.330  -0.254  1.00  0.00           H  
HETATM   37  H7  UNL     1      -5.268  -1.243  -0.728  1.00  0.00           H  
HETATM   38  H8  UNL     1      -5.759  -1.487   0.926  1.00  0.00           H  
HETATM   39  H9  UNL     1      -3.445  -1.984   0.703  1.00  0.00           H  
HETATM   40  H10 UNL     1      -3.820  -0.791   1.936  1.00  0.00           H  
HETATM   41  H11 UNL     1      -2.572  -0.195  -0.810  1.00  0.00           H  
HETATM   42  H12 UNL     1      -3.646   1.789   0.996  1.00  0.00           H  
HETATM   43  H13 UNL     1      -2.465   1.996  -0.309  1.00  0.00           H  
HETATM   44  H14 UNL     1      -1.986   1.577   1.445  1.00  0.00           H  
HETATM   45  H15 UNL     1      -1.282  -0.550   1.929  1.00  0.00           H  
HETATM   46  H16 UNL     1      -1.651  -2.748   1.196  1.00  0.00           H  
HETATM   47  H17 UNL     1      -1.879  -2.265  -0.547  1.00  0.00           H  
HETATM   48  H18 UNL     1       0.448  -3.325   0.644  1.00  0.00           H  
HETATM   49  H19 UNL     1       0.375  -2.666  -0.994  1.00  0.00           H  
HETATM   50  H20 UNL     1       0.945  -1.259   1.632  1.00  0.00           H  
HETATM   51  H21 UNL     1       2.325  -1.184  -1.113  1.00  0.00           H  
HETATM   52  H22 UNL     1       2.777  -3.117   0.446  1.00  0.00           H  
HETATM   53  H23 UNL     1       3.125  -1.827   1.723  1.00  0.00           H  
HETATM   54  H24 UNL     1       5.189  -2.720   0.121  1.00  0.00           H  
HETATM   55  H25 UNL     1       6.809  -1.532  -0.810  1.00  0.00           H  
HETATM   56  H26 UNL     1       6.381  -0.098  -1.756  1.00  0.00           H  
HETATM   57  H27 UNL     1       7.624  -0.324   0.932  1.00  0.00           H  
HETATM   58  H28 UNL     1       8.798   0.724  -0.462  1.00  0.00           H  
HETATM   59  H29 UNL     1       5.723   0.529   1.995  1.00  0.00           H  
HETATM   60  H30 UNL     1       6.623   1.989   1.551  1.00  0.00           H  
HETATM   61  H31 UNL     1       4.241   2.156   1.119  1.00  0.00           H  
HETATM   62  H32 UNL     1       5.226   2.431  -0.331  1.00  0.00           H  
HETATM   63  H33 UNL     1       3.526   2.118  -1.621  1.00  0.00           H  
HETATM   64  H34 UNL     1       4.763   1.030  -2.272  1.00  0.00           H  
HETATM   65  H35 UNL     1       3.032   0.419  -2.162  1.00  0.00           H  
HETATM   66  H36 UNL     1       2.888   0.289   1.511  1.00  0.00           H  
HETATM   67  H37 UNL     1       2.246   2.360   0.446  1.00  0.00           H  
HETATM   68  H38 UNL     1       1.664   1.549  -1.015  1.00  0.00           H  
HETATM   69  H39 UNL     1      -0.125   2.086   0.293  1.00  0.00           H  
HETATM   70  H40 UNL     1       0.536   1.153   1.753  1.00  0.00           H  
HETATM   71  H41 UNL     1      -0.962   0.727  -1.656  1.00  0.00           H  
HETATM   72  H42 UNL     1      -0.704  -1.081  -1.639  1.00  0.00           H  
HETATM   73  H43 UNL     1       0.663   0.004  -1.888  1.00  0.00           H  
HETATM   74  H44 UNL     1      -7.662  -1.933  -1.790  1.00  0.00           H  
CONECT    1    2   31   32   33
CONECT    2    3   28   34
CONECT    3    4   35   36
CONECT    4    5   37   38
CONECT    5    6   39   40
CONECT    6    7    8   41
CONECT    7   42   43   44
CONECT    8    9   26   45
CONECT    9   10   46   47
CONECT   10   11   48   49
CONECT   11   12   26   50
CONECT   12   13   23   51
CONECT   13   14   52   53
CONECT   14   15   15   54
CONECT   15   16   21
CONECT   16   17   55   56
CONECT   17   18   19   57
CONECT   18   58
CONECT   19   20   59   60
CONECT   20   21   61   62
CONECT   21   22   23
CONECT   22   63   64   65
CONECT   23   24   66
CONECT   24   25   67   68
CONECT   25   26   69   70
CONECT   26   27
CONECT   27   71   72   73
CONECT   28   29   29   30
CONECT   30   74
END

HMDB0012453
     RDKit          3D
3beta-Hydroxy-5-cholestenoic acid
 74 77  0  0  0  0  0  0  0  0999 V2000
   -7.8493    1.9046    0.1077 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2607    0.4916   -0.0717 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.8061    0.5336    0.4087 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1247   -0.7663    0.2975 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7593   -0.8886    0.7940 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6421   -0.0716    0.3201 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7169    1.3890    0.5742 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3349   -0.6400    0.8499 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2733   -2.0988    0.3570 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1475   -2.4152    0.0508 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8782   -1.1867    0.5271 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2395   -1.0447   -0.0324 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1220   -2.0832    0.6276 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5106   -1.8588    0.1400 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9300   -0.6652   -0.2621 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3357   -0.5478   -0.7308 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0445    0.3662    0.2616 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.9194    1.1817   -0.4219 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0798    1.1120    1.1346 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8906    1.6564    0.3851 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0813    0.5574   -0.2717 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8096    1.0307   -1.7053 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7767    0.3160    0.4133 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8234    1.4068    0.0664 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4258    1.1864    0.6678 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1066   -0.0974    0.1520 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3175   -0.0911   -1.3438 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4274    0.1211   -1.4675 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9022    0.9754   -2.2925 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1213   -1.1026   -2.0463 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4071    2.4160    0.9661 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9421    1.7885    0.1793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6471    2.4418   -0.8399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8873   -0.1690    0.5599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8187    0.9271    1.4289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3710    1.3298   -0.2542 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2678   -1.2430   -0.7278 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7592   -1.4875    0.9256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4449   -1.9845    0.7032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8196   -0.7915    1.9362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5723   -0.1948   -0.8100 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6460    1.7889    0.9963 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4654    1.9960   -0.3087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9861    1.5769    1.4445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2823   -0.5496    1.9291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6512   -2.7479    1.1960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8790   -2.2647   -0.5470 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4480   -3.3248    0.6442 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3755   -2.6664   -0.9943 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9454   -1.2585    1.6319 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3250   -1.1835   -1.1135 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7766   -3.1171    0.4458 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1247   -1.8273    1.7233 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1895   -2.7201    0.1215 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8090   -1.5315   -0.8105 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3809   -0.0982   -1.7562 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6236   -0.3242    0.9320 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7977    0.7241   -0.4615 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7230    0.5286    1.9946 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6231    1.9888    1.5506 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2405    2.1561    1.1187 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2256    2.4309   -0.3315 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5265    2.1184   -1.6213 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7631    1.0302   -2.2719 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0321    0.4187   -2.1624 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8882    0.2890    1.5109 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2458    2.3599    0.4465 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6644    1.5485   -1.0149 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1252    2.0858    0.2926 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5365    1.1530    1.7533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9620    0.7266   -1.6561 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7037   -1.0812   -1.6389 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6631    0.0042   -1.8882 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6621   -1.9334   -1.7896 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  6
 21 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  1  6
  2 28  1  0
 28 29  2  0
 28 30  1  0
 26  8  1  0
 26 11  1  0
 23 12  1  0
 21 15  1  0
  1 31  1  0
  1 32  1  0
  1 33  1  0
  2 34  1  1
  3 35  1  0
  3 36  1  0
  4 37  1  0
  4 38  1  0
  5 39  1  0
  5 40  1  0
  6 41  1  6
  7 42  1  0
  7 43  1  0
  7 44  1  0
  8 45  1  1
  9 46  1  0
  9 47  1  0
 10 48  1  0
 10 49  1  0
 11 50  1  1
 12 51  1  6
 13 52  1  0
 13 53  1  0
 14 54  1  0
 16 55  1  0
 16 56  1  0
 17 57  1  1
 18 58  1  0
 19 59  1  0
 19 60  1  0
 20 61  1  0
 20 62  1  0
 22 63  1  0
 22 64  1  0
 22 65  1  0
 23 66  1  1
 24 67  1  0
 24 68  1  0
 25 69  1  0
 25 70  1  0
 27 71  1  0
 27 72  1  0
 27 73  1  0
 30 74  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
3b-Hydroxy-5-cholestenoate	Generator
3b-Hydroxy-5-cholestenoic acid	Generator
3beta-Hydroxy-5-cholestenoate	Generator
3Β-hydroxy-5-cholestenoate	Generator
3Β-hydroxy-5-cholestenoic acid	Generator
5-Cholesten-3-ol-25-carboxylic acid	HMDB
(25R)-3b-Hydroxycholest-5-en-26-Oate	HMDB
(25R)-3b-Hydroxycholest-5-en-26-Oic acid	HMDB
(25R)-3beta-Hydroxycholest-5-en-26-Oate	HMDB
(25R)-3Β-hydroxycholest-5-en-26-Oate	HMDB
(25R)-3Β-hydroxycholest-5-en-26-Oic acid	HMDB
(3beta)-3-Hydroxycholest-5-en-26-Oic acid	HMDB
(3beta,25R)-3-Hydroxycholest-5-en-26-Oic acid	HMDB
(3Β)-3-hydroxycholest-5-en-26-Oic acid	HMDB
(3Β,25R)-3-hydroxycholest-5-en-26-Oic acid	HMDB
3beta-Hydroxycholest-5-en-26-Oic acid	HMDB
3beta-Hydroxycholest-5-en-27-Oic acid	HMDB
3Β-hydroxycholest-5-en-26-Oic acid	HMDB
3Β-hydroxycholest-5-en-27-Oic acid	HMDB
3beta-Hydroxy-5-cholestenoic acid	HMDB

Chemical Formula

C₂₇H₄₄O₃

Average Molecular Weight

416.646

Monoisotopic Molecular Weight

416.329045277

IUPAC Name

(2R,6R)-6-[(1S,2R,5S,10S,11S,14R,15R)-5-hydroxy-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-7-en-14-yl]-2-methylheptanoic acid

Traditional Name

(2R,6R)-6-[(1S,2R,5S,10S,11S,14R,15R)-5-hydroxy-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-7-en-14-yl]-2-methylheptanoic acid

CAS Registry Number

56845-87-5

SMILES

[H][C@@]1(CC[C@@]2([H])[C@]3([H])CC=C4C[C@@H](O)CC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCC[C@@H](C)C(O)=O

InChI Identifier

InChI=1S/C27H44O3/c1-17(6-5-7-18(2)25(29)30)22-10-11-23-21-9-8-19-16-20(28)12-14-26(19,3)24(21)13-15-27(22,23)4/h8,17-18,20-24,28H,5-7,9-16H2,1-4H3,(H,29,30)/t17-,18-,20+,21+,22-,23+,24+,26+,27-/m1/s1

InChI Key

WVXOMPRLWLXFAP-KQOPCUSDSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monohydroxy bile acids, alcohols and derivatives. These are bile acids, alcohols or any of their derivatives bearing a hydroxyl group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Bile acids, alcohols and derivatives

Direct Parent

Monohydroxy bile acids, alcohols and derivatives

Alternative Parents

Substituents

Monohydroxy bile acid, alcohol, or derivatives
Steroid acid
3-hydroxy-delta-5-steroid
3-hydroxysteroid
3-beta-hydroxysteroid
3-beta-hydroxy-delta-5-steroid
Hydroxysteroid
Delta-5-steroid
Medium-chain fatty acid
Hydroxy fatty acid
Fatty acyl
Cyclic alcohol
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Organic oxide
Organic oxygen compound
Carbonyl group
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

3beta-hydroxycholest-5-en-26-oic acid (CHEBI:86378 )
C27 bile acids, alcohols, and derivatives (LMST04030072 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31477923)

Cellular substructure

Extracellular (HMDB: HMDB0012453)
Membrane (HMDB: HMDB0012453)

Source

Endogenous

Endogenous (HMDB: HMDB0012453)

Exogenous

Exogenous (HMDB: HMDB0012453)

Food

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)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Bile Acid Biosynthesis (HMDB: HMDB0012453)

Disease pathway

Congenital Bile Acid Synthesis Defect Type III (HMDB: HMDB0012453)
27-Hydroxylase Deficiency (PathBank: SMP0120652)
Cerebrotendinous Xanthomatosis (CTX) (PathBank: SMP0120683)
Familial Hypercholanemia (FHCA) (PathBank: SMP0120697)
Zellweger Syndrome (PathBank: SMP0120715)
Congenital Bile Acid Synthesis Defect Type II (PathBank: SMP0120687)

Role

Not Available

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

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.00048 g/L	ALOGPS
logP	5.57	ALOGPS
logP	6.05	ChemAxon
logS	-5.9	ALOGPS
pKa (Strongest Acidic)	4.83	ChemAxon
pKa (Strongest Basic)	-1.4	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.53 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	122.31 m³·mol⁻¹	ChemAxon
Polarizability	51.55 Å³	ChemAxon
Number of Rings	4	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
DeepCCS	[M-2H]-	241.137	30932474
DeepCCS	[M+Na]+	215.57	30932474
AllCCS	[M+H]+	208.2	32859911
AllCCS	[M+H-H2O]+	206.3	32859911
AllCCS	[M+NH4]+	210.0	32859911
AllCCS	[M+Na]+	210.5	32859911
AllCCS	[M-H]-	205.0	32859911
AllCCS	[M+Na-2H]-	206.9	32859911
AllCCS	[M+HCOO]-	209.2	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.	9.14 minutes	32390414
Predicted by Siyang on May 30, 2022	21.3978 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.44 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	52.1 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	3331.5 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	491.2 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	264.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	205.5 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	633.7 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	941.2 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	893.0 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	107.7 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1678.9 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	630.9 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	1886.4 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	558.2 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	553.5 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	249.7 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	514.5 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
3beta-Hydroxy-5-cholestenoic acid	[H][C@@]1(CC[C@@]2([H])[C@]3([H])CC=C4C[C@@H](O)CC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCC[C@@H](C)C(O)=O	3572.9	Standard polar	33892256
3beta-Hydroxy-5-cholestenoic acid	[H][C@@]1(CC[C@@]2([H])[C@]3([H])CC=C4C[C@@H](O)CC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCC[C@@H](C)C(O)=O	3409.5	Standard non polar	33892256
3beta-Hydroxy-5-cholestenoic acid	[H][C@@]1(CC[C@@]2([H])[C@]3([H])CC=C4C[C@@H](O)CC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCC[C@@H](C)C(O)=O	3525.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3beta-Hydroxy-5-cholestenoic acid,1TMS,isomer #1	C[C@H](CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@@H](O[Si](C)(C)C)CC[C@]4(C)[C@H]3CC[C@@]21C)C(=O)O	3596.2	Semi standard non polar	33892256
3beta-Hydroxy-5-cholestenoic acid,1TMS,isomer #2	C[C@H](CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@@]21C)C(=O)O[Si](C)(C)C	3480.7	Semi standard non polar	33892256
3beta-Hydroxy-5-cholestenoic acid,2TMS,isomer #1	C[C@H](CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@@H](O[Si](C)(C)C)CC[C@]4(C)[C@H]3CC[C@@]21C)C(=O)O[Si](C)(C)C	3498.5	Semi standard non polar	33892256
3beta-Hydroxy-5-cholestenoic acid,1TBDMS,isomer #1	C[C@H](CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@@H](O[Si](C)(C)C(C)(C)C)CC[C@]4(C)[C@H]3CC[C@@]21C)C(=O)O	3813.7	Semi standard non polar	33892256
3beta-Hydroxy-5-cholestenoic acid,1TBDMS,isomer #2	C[C@H](CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@@]21C)C(=O)O[Si](C)(C)C(C)(C)C	3756.1	Semi standard non polar	33892256
3beta-Hydroxy-5-cholestenoic acid,2TBDMS,isomer #1	C[C@H](CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@@H](O[Si](C)(C)C(C)(C)C)CC[C@]4(C)[C@H]3CC[C@@]21C)C(=O)O[Si](C)(C)C(C)(C)C	4025.8	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 3beta-Hydroxy-5-cholestenoic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3beta-Hydroxy-5-cholestenoic acid 10V, Negative-QTOF	splash10-014i-0001900000-9291456af111b57a086a	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3beta-Hydroxy-5-cholestenoic acid 20V, Negative-QTOF	splash10-014i-0007900000-53d9c33626532c025532	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3beta-Hydroxy-5-cholestenoic acid 40V, Negative-QTOF	splash10-03di-2003900000-44ce8c22a104fa8cb7d5	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3beta-Hydroxy-5-cholestenoic acid 10V, Positive-QTOF	splash10-014j-1109500000-59889f5826d4841604c0	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3beta-Hydroxy-5-cholestenoic acid 20V, Positive-QTOF	splash10-0ff0-2169000000-925cc86a36a9e049df54	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3beta-Hydroxy-5-cholestenoic acid 40V, Positive-QTOF	splash10-0a4m-7910000000-ffc877d5e91fdf1f8c9d	2021-09-22	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Name	SMPDB/PathBank	KEGG
Primary bile acid biosynthesis	Not Available
Congenital Bile Acid Synthesis Defect Type II		Not Available
Congenital Bile Acid Synthesis Defect Type III		Not Available
Familial Hypercholanemia (FHCA)		Not Available
Zellweger Syndrome		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	31477923	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB111635

KNApSAcK ID

Not Available

Chemspider ID

25942571

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

40579073

PDB ID

Not Available

ChEBI ID

86378

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
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 ]
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 ]
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 ]
Wilmanski T, Rappaport N, Earls JC, Magis AT, Manor O, Lovejoy J, Omenn GS, Hood L, Gibbons SM, Price ND: Blood metabolome predicts gut microbiome alpha-diversity in humans. Nat Biotechnol. 2019 Oct;37(10):1217-1228. doi: 10.1038/s41587-019-0233-9. Epub 2019 Sep 2. [PubMed:31477923 ]
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Enzymes

Enzyme Details

1. Sterol 26-hydroxylase, mitochondrial

General function:: Involved in monooxygenase activity
Specific function:: Catalyzes the first step in the oxidation of the side chain of sterol intermediates; the 27-hydroxylation of 5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol. Has also a vitamin D3-25-hydroxylase activity.
Gene Name:: CYP27A1
Uniprot ID:: Q02318
Molecular weight:: 60234.28

Reactions

27-Hydroxycholesterol + Oxygen + NADPH + Hydrogen Ion → 3beta-Hydroxy-5-cholestenoic acid + NADP + Water	details

Enzyme Details

2. 25-hydroxycholesterol 7-alpha-hydroxylase

General function:: Involved in monooxygenase activity
Specific function:: Not Available
Gene Name:: CYP7B1
Uniprot ID:: O75881
Molecular weight:: 58255.325

Reactions

3beta-Hydroxy-5-cholestenoic acid + Oxygen + NADPH + Hydrogen Ion → 3beta,7alpha-Dihydroxy-5-cholestenoate + NADP + Water	details

Showing metabocard for 3beta-Hydroxy-5-cholestenoic acid (HMDB0012453)

MOL for HMDB0012453 (3beta-Hydroxy-5-cholestenoic acid)

3D MOL for HMDB0012453 (3beta-Hydroxy-5-cholestenoic acid)

3D SDF for HMDB0012453 (3beta-Hydroxy-5-cholestenoic acid)

3D-SDF for HMDB0012453 (3beta-Hydroxy-5-cholestenoic acid)

PDB for HMDB0012453 (3beta-Hydroxy-5-cholestenoic acid)

3D PDB for HMDB0012453 (3beta-Hydroxy-5-cholestenoic acid)

SMILES for HMDB0012453 (3beta-Hydroxy-5-cholestenoic acid)

INCHI for HMDB0012453 (3beta-Hydroxy-5-cholestenoic acid)

Structure for HMDB0012453 (3beta-Hydroxy-5-cholestenoic acid)

3D Structure for HMDB0012453 (3beta-Hydroxy-5-cholestenoic acid)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

Enzymes

Reactions

Reactions