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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2009-07-13 12:02:10 UTC
Update Date2021-09-14 15:19:06 UTC
HMDB IDHMDB0012453
Secondary Accession Numbers
  • HMDB12453
Metabolite Identification
Common Name3beta-Hydroxy-5-cholestenoic acid
Description3beta-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
Data?1582753056
Synonyms
ValueSource
3b-Hydroxy-5-cholestenoateGenerator
3b-Hydroxy-5-cholestenoic acidGenerator
3beta-Hydroxy-5-cholestenoateGenerator
3Β-hydroxy-5-cholestenoateGenerator
3Β-hydroxy-5-cholestenoic acidGenerator
5-Cholesten-3-ol-25-carboxylic acidMeSH
(25R)-3b-Hydroxycholest-5-en-26-OateGenerator, HMDB
(25R)-3b-Hydroxycholest-5-en-26-Oic acidGenerator, HMDB
(25R)-3beta-Hydroxycholest-5-en-26-OateGenerator, HMDB
(25R)-3Β-hydroxycholest-5-en-26-OateGenerator, HMDB
(25R)-3Β-hydroxycholest-5-en-26-Oic acidGenerator, HMDB
(3beta)-3-Hydroxycholest-5-en-26-oic acidHMDB
(3beta,25R)-3-Hydroxycholest-5-en-26-oic acidHMDB
(3β)-3-Hydroxycholest-5-en-26-oic acidHMDB
(3β,25R)-3-Hydroxycholest-5-en-26-oic acidHMDB
3beta-Hydroxy-5-cholestenoic acidHMDB
3beta-Hydroxycholest-5-en-26-oic acidHMDB
3beta-Hydroxycholest-5-en-27-oic acidHMDB
3β-Hydroxycholest-5-en-26-oic acidHMDB
3β-Hydroxycholest-5-en-27-oic acidHMDB
Chemical FormulaC27H44O3
Average Molecular Weight416.646
Monoisotopic Molecular Weight416.329045277
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 Number56845-87-5
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 KeyWVXOMPRLWLXFAP-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.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSteroids and steroid derivatives
Sub ClassBile acids, alcohols and derivatives
Direct ParentMonohydroxy 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 FrameworkAliphatic homopolycyclic compounds
External Descriptors
Ontology
Disposition

Biological location

Source

Route of exposure

Process

Naturally occurring process

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Spectral PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.00048 g/LALOGPS
logP10(5.57) g/LALOGPS
logP10(6.05) g/LChemAxon
logS10(-5.9) g/LALOGPS
pKa (Strongest Acidic)4.83ChemAxon
pKa (Strongest Basic)-1.4ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity122.31 m³·mol⁻¹ChemAxon
Polarizability51.55 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Spectral Properties

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3beta-Hydroxy-5-cholestenoic acid,1TMS,#1C[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)O3596.2Semi standard non polarhttps://arxiv.org/abs/1905.12712
3beta-Hydroxy-5-cholestenoic acid,1TMS,#2C[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)C3480.7Semi standard non polarhttps://arxiv.org/abs/1905.12712
3beta-Hydroxy-5-cholestenoic acid,2TMS,#1C[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)C3498.5Semi standard non polarhttps://arxiv.org/abs/1905.12712
3beta-Hydroxy-5-cholestenoic acid,1TBDMS,#1C[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)O3813.7Semi standard non polarhttps://arxiv.org/abs/1905.12712
3beta-Hydroxy-5-cholestenoic acid,1TBDMS,#2C[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)C3756.1Semi standard non polarhttps://arxiv.org/abs/1905.12712
3beta-Hydroxy-5-cholestenoic acid,2TBDMS,#1C[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)C4025.8Semi standard non polarhttps://arxiv.org/abs/1905.12712
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3beta-Hydroxy-5-cholestenoic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3beta-Hydroxy-5-cholestenoic acid 10V, Negative-QTOFsplash10-014i-0001900000-9291456af111b57a086a2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3beta-Hydroxy-5-cholestenoic acid 20V, Negative-QTOFsplash10-014i-0007900000-53d9c33626532c0255322021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3beta-Hydroxy-5-cholestenoic acid 40V, Negative-QTOFsplash10-03di-2003900000-44ce8c22a104fa8cb7d52021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3beta-Hydroxy-5-cholestenoic acid 10V, Positive-QTOFsplash10-014j-1109500000-59889f5826d4841604c02021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3beta-Hydroxy-5-cholestenoic acid 20V, Positive-QTOFsplash10-0ff0-2169000000-925cc86a36a9e049df542021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3beta-Hydroxy-5-cholestenoic acid 40V, Positive-QTOFsplash10-0a4m-7910000000-ffc877d5e91fdf1f8c9d2021-09-22Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB111635
KNApSAcK IDNot Available
Chemspider ID25942571
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound40579073
PDB IDNot Available
ChEBI ID86378
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  3. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  4. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  5. 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 ]
  6. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Enzymes

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 + Waterdetails
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 + Waterdetails