Hmdb loader
You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2007-05-22 17:50:52 UTC
Update Date2022-03-07 02:49:30 UTC
HMDB IDHMDB0006217
Secondary Accession Numbers
  • HMDB06217
Metabolite Identification
Common Name9-cis-Retinol
Description9-cis-retinol is a retinoid. Retinoids (vitamin A and its analogs) are essential dietary substances that are needed by mammals for reproduction, normal embryogenesis, growth, vision, and maintaining normal cellular differentiation and the integrity of the immune system. Within cells, retinoids regulate gene transcription acting through ligand-dependent transcription factors, the retinoic acid receptors (RARs), and the retinoid X receptors (RXRs). All-trans-retinoic acid binds only to RARs with high affinity, whereas its 9-cis isomer binds with high affinity to both RARs and RXRs. The actions of all-trans- and 9-cis-retinoic acid in regulating cellular responses are distinct and not interchangeable. (PMID: 9115228 ).
Structure
Data?1582752375
Synonyms
ValueSource
(2E,4E,6Z,8E)-3,7-Dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraen-1-olChEBI
(9cis)-RetinolChEBI
9-cis RetinolHMDB
Chemical FormulaC20H30O
Average Molecular Weight286.4516
Monoisotopic Molecular Weight286.229665582
IUPAC Name(2E,4E,6Z,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraen-1-ol
Traditional Name9-cis-retinol
CAS Registry Number22737-97-9
SMILES
C\C(=C/CO)\C=C\C=C(\C)/C=C/C1=C(C)CCCC1(C)C
InChI Identifier
InChI=1S/C20H30O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,21H,7,10,14-15H2,1-5H3/b9-6+,12-11+,16-8-,17-13+
InChI KeyFPIPGXGPPPQFEQ-MKOSUFFBSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as retinoids. These are oxygenated derivatives of 3,7-dimethyl-1-(2,6,6-trimethylcyclohex-1-enyl)nona-1,3,5,7-tetraene and derivatives thereof.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassRetinoids
Direct ParentRetinoids
Alternative Parents
Substituents
  • Retinoid skeleton
  • Diterpenoid
  • Fatty alcohol
  • Fatty acyl
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Alcohol
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.0076 g/LALOGPS
logP6.38ALOGPS
logP4.69ChemAxon
logS-4.6ALOGPS
pKa (Strongest Acidic)16.44ChemAxon
pKa (Strongest Basic)-2.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area20.23 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity97.92 m³·mol⁻¹ChemAxon
Polarizability35.86 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+176.39631661259
DarkChem[M-H]-173.27331661259
DeepCCS[M+H]+186.23330932474
DeepCCS[M-H]-183.87530932474
DeepCCS[M-2H]-217.55130932474
DeepCCS[M+Na]+192.77730932474
AllCCS[M+H]+174.332859911
AllCCS[M+H-H2O]+171.132859911
AllCCS[M+NH4]+177.332859911
AllCCS[M+Na]+178.232859911
AllCCS[M-H]-179.732859911
AllCCS[M+Na-2H]-180.432859911
AllCCS[M+HCOO]-181.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
9-cis-RetinolC\C(=C/CO)\C=C\C=C(\C)/C=C/C1=C(C)CCCC1(C)C3108.0Standard polar33892256
9-cis-RetinolC\C(=C/CO)\C=C\C=C(\C)/C=C/C1=C(C)CCCC1(C)C2431.2Standard non polar33892256
9-cis-RetinolC\C(=C/CO)\C=C\C=C(\C)/C=C/C1=C(C)CCCC1(C)C2417.0Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
9-cis-Retinol,1TMS,isomer #1CC1=C(/C=C/C(C)=C\C=C\C(C)=C\CO[Si](C)(C)C)C(C)(C)CCC12597.7Semi standard non polar33892256
9-cis-Retinol,1TBDMS,isomer #1CC1=C(/C=C/C(C)=C\C=C\C(C)=C\CO[Si](C)(C)C(C)(C)C)C(C)(C)CCC12794.8Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 9-cis-Retinol GC-MS (Non-derivatized) - 70eV, Positivesplash10-00di-1190000000-346a3e44c44d46353e802017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 9-cis-Retinol GC-MS (1 TMS) - 70eV, Positivesplash10-0006-7139000000-7242603c3f7f12c824cd2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 9-cis-Retinol 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 - 9-cis-Retinol 10V, Positive-QTOFsplash10-00kr-0490000000-97ed49d705440e4d32e72016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinol 20V, Positive-QTOFsplash10-00ks-3930000000-7c5bfbd8b838b97dc2aa2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinol 40V, Positive-QTOFsplash10-0fri-9820000000-6a49bab0c891ffe1e5b22016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinol 10V, Negative-QTOFsplash10-000i-0090000000-d0ff1cdc72141d0daa0e2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinol 20V, Negative-QTOFsplash10-0a4r-0090000000-c0a067ff8ed271b809452016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinol 40V, Negative-QTOFsplash10-00ku-4590000000-cfc35aba420e707075f72016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinol 10V, Negative-QTOFsplash10-0a4i-0090000000-fe93459d3069e264b77f2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinol 20V, Negative-QTOFsplash10-05mx-0190000000-f81760535f6050971f922021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinol 40V, Negative-QTOFsplash10-00li-0960000000-4dbc516b202b90a6c2652021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinol 10V, Positive-QTOFsplash10-015i-1890000000-fb68e645ac6c84dc722c2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinol 20V, Positive-QTOFsplash10-05a9-2910000000-aa07b89a9cfe132b87252021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinol 40V, Positive-QTOFsplash10-06dl-5900000000-6de72efc591b252620c92021-09-22Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB010848
KNApSAcK IDNot Available
Chemspider ID8123435
KEGG Compound IDC16682
BioCyc IDNot Available
BiGG ID2265507
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound9947823
PDB IDNot Available
ChEBI ID78272
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceOediger, Hermann; Eiter, Karl. 9-cis-Vitamin A and its esters. (1963), 5 pp. DE 1157606 19631121 CAN 60:31181 AN 1964:31181
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Mertz JR, Shang E, Piantedosi R, Wei S, Wolgemuth DJ, Blaner WS: Identification and characterization of a stereospecific human enzyme that catalyzes 9-cis-retinol oxidation. A possible role in 9-cis-retinoic acid formation. J Biol Chem. 1997 May 2;272(18):11744-9. [PubMed:9115228 ]