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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2007-05-22 18:00:08 UTC
Update Date2022-03-07 02:49:30 UTC
HMDB IDHMDB0006221
Secondary Accession Numbers
  • HMDB06221
Metabolite Identification
Common Name13-cis Retinol
Description13-cis Retinol is a retinoid inapplicable to the visual processes, and therefore it could be an important catabolic metabolite and its biosynthesis could be part of a process involved in regulating 11-cis-retinol concentrations within the retinal pigment epithelium of 11-cis-retinol dehydrogenase. 13-cis Retinol accumulates as a consequence of reduced 11-cis-retinol oxidation capacity. Reduced 11-cis-retinol oxidation occurs in 11-cis-Retinol dehydrogenase deficiency. Mutations in the 11-cis-retinol dehydrogenase gene in humans have been associated with fundus albipunctatus (delayed dark adaptation and punctata are typical symptoms of this human hereditary ocular disease). (PMID: 10825191 ).
Structure
Data?1582752375
Synonyms
ValueSource
(13cis)-RetinolChEBI
(2Z,4E,6E,8E)-3,7-Dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraen-1-olChEBI
RETINOLChEBI
Neovitamin aKegg
(11-cis,13-cis)-Retinol acetateHMDB
11,13-Di-cis-vitamin a acetateHMDB
11-cis-13-cis-Retinol acetateHMDB
11-cis-13-cis-Retinyl acetateHMDB
Chemical FormulaC20H30O
Average Molecular Weight286.4516
Monoisotopic Molecular Weight286.229665582
IUPAC Name(2Z,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraen-1-ol
Traditional Name13-cis retinol
CAS Registry Number2052-63-3
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-HWCYFHEPSA-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
ProcessNot Available
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
Polarizability36.28 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]+176.08931661259
DarkChem[M-H]-173.49931661259
DeepCCS[M+H]+184.48530932474
DeepCCS[M-H]-182.12730932474
DeepCCS[M-2H]-215.75830932474
DeepCCS[M+Na]+190.98430932474
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
13-cis RetinolC\C(=C\CO)\C=C\C=C(/C)\C=C\C1=C(C)CCCC1(C)C3108.0Standard polar33892256
13-cis RetinolC\C(=C\CO)\C=C\C=C(/C)\C=C\C1=C(C)CCCC1(C)C2431.2Standard non polar33892256
13-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
13-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
13-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 - 13-cis Retinol GC-MS (Non-derivatized) - 70eV, Positivesplash10-00di-1190000000-346a3e44c44d46353e802017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 13-cis Retinol GC-MS (1 TMS) - 70eV, Positivesplash10-0006-7139000000-7242603c3f7f12c824cd2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 13-cis Retinol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
MSMass Spectrum (Electron Ionization)splash10-052r-2950000000-c24ec8ff8d0ba6c1f23f2018-05-25Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - 13-cis Retinol Quattro_QQQ 10V, Positive-QTOF (Annotated)splash10-000i-0290000000-25c523b646154b291da82018-05-25HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 13-cis Retinol Quattro_QQQ 25V, Positive-QTOF (Annotated)splash10-05gj-3900000000-a63c286f931608f650a32018-05-25HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 13-cis Retinol Quattro_QQQ 40V, Positive-QTOF (Annotated)splash10-05mo-9700000000-e627db30469c74bb037f2018-05-25HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis Retinol 10V, Positive-QTOFsplash10-00kr-1490000000-7205fba02aeb80622df82017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis Retinol 20V, Positive-QTOFsplash10-00m0-3920000000-951836eaf171751b137c2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis Retinol 40V, Positive-QTOFsplash10-0lei-9810000000-b9b76a3e956e61a7d39e2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis Retinol 10V, Negative-QTOFsplash10-000i-0090000000-575d71f5f53354f828c22017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis Retinol 20V, Negative-QTOFsplash10-0a4r-0090000000-c71c47589510cf7c1a0b2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis Retinol 40V, Negative-QTOFsplash10-00ku-3690000000-26f7587a1f34c10cd8f72017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis Retinol 10V, Negative-QTOFsplash10-0a4i-0090000000-fe93459d3069e264b77f2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis Retinol 20V, Negative-QTOFsplash10-05mx-0190000000-f81760535f6050971f922021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis Retinol 40V, Negative-QTOFsplash10-00li-0960000000-4dbc516b202b90a6c2652021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis Retinol 10V, Positive-QTOFsplash10-015i-1890000000-fb68e645ac6c84dc722c2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis Retinol 20V, Positive-QTOFsplash10-05a9-2910000000-aa07b89a9cfe132b87252021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis Retinol 40V, Positive-QTOFsplash10-06dl-5900000000-6de72efc591b252620c92021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, CDCl3, experimental)2018-05-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biospecimen Locations
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB112229
KNApSAcK IDNot Available
Chemspider ID8079655
KEGG Compound IDC19962
BioCyc IDNot Available
BiGG ID2455099
Wikipedia LinkVitamin A
METLIN IDNot Available
PubChem Compound9904001
PDB IDNot Available
ChEBI ID45479
Food Biomarker OntologyNot Available
VMH IDRETINOL_CIS_13
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceAlbert, Klaus; Schlotterbeck, Goetz; Braumann, Ulrich; Haendel, Heidrun; Spraul, Manfred; Krack, Gerhard. Structure determination of vitamin A acetate isomers through coupled HPLC and 1H NMR spectroscopy. Angewandte Chemie, International Edition in English (1995), 34(9), 1014-16.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Driessen CA, Winkens HJ, Hoffmann K, Kuhlmann LD, Janssen BP, Van Vugt AH, Van Hooser JP, Wieringa BE, Deutman AF, Palczewski K, Ruether K, Janssen JJ: Disruption of the 11-cis-retinol dehydrogenase gene leads to accumulation of cis-retinols and cis-retinyl esters. Mol Cell Biol. 2000 Jun;20(12):4275-87. [PubMed:10825191 ]