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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-03-21 06:15:37 UTC
Update Date2021-09-14 15:46:22 UTC
HMDB IDHMDB0062411
Secondary Accession Numbers
  • HMDB62411
Metabolite Identification
Common Name5,6-Epoxy-13-cis-retinoic acid
Description81444-57-7 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. 81444-57-7 is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Data?1563866308
Synonyms
ValueSource
5,6-Epoxy-13-cis-retinoateGenerator
13-cis-5,6-Epoxy-5,6-dihydroretinoic acidHMDB
Chemical FormulaC20H28O3
Average Molecular Weight316.441
Monoisotopic Molecular Weight316.203844762
IUPAC Name(2Z,4E,6E,8E)-3,7-dimethyl-9-{2,2,6-trimethyl-7-oxabicyclo[4.1.0]heptan-1-yl}nona-2,4,6,8-tetraenoic acid
Traditional Name(2Z,4E,6E,8E)-3,7-dimethyl-9-{2,2,6-trimethyl-7-oxabicyclo[4.1.0]heptan-1-yl}nona-2,4,6,8-tetraenoic acid
CAS Registry Number81444-57-7
SMILES
C\C(\C=C\C12OC1(C)CCCC2(C)C)=C/C=C/C(/C)=C\C(O)=O
InChI Identifier
InChI=1S/C20H28O3/c1-15(8-6-9-16(2)14-17(21)22)10-13-20-18(3,4)11-7-12-19(20,5)23-20/h6,8-10,13-14H,7,11-12H2,1-5H3,(H,21,22)/b9-6+,13-10+,15-8+,16-14-
InChI KeyKEEHJLBAOLGBJZ-NJZIYGCESA-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
  • Retinoic acid
  • Diterpenoid
  • Retinoid skeleton
  • Medium-chain fatty acid
  • Branched fatty acid
  • Epoxy fatty acid
  • Heterocyclic fatty acid
  • Oxepane
  • Methyl-branched fatty acid
  • Unsaturated fatty acid
  • Fatty acyl
  • Fatty acid
  • Carboxylic acid derivative
  • Organoheterocyclic compound
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Ether
  • Oxacycle
  • Oxirane
  • Dialkyl ether
  • Hydrocarbon derivative
  • Organic oxygen compound
  • Carbonyl group
  • Organooxygen compound
  • Organic oxide
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
DispositionNot Available
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
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
logP5.74ALOGPS
logP4.54ChemAxon
logS-4.9ALOGPS
pKa (Strongest Acidic)4.94ChemAxon
pKa (Strongest Basic)-4.3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area49.83 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity96.52 m³·mol⁻¹ChemAxon
Polarizability36.97 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M-2H]-228.38230932474
DeepCCS[M+Na]+203.60930932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5,6-Epoxy-13-cis-retinoic acidC\C(\C=C\C12OC1(C)CCCC2(C)C)=C/C=C/C(/C)=C\C(O)=O3855.1Standard polar33892256
5,6-Epoxy-13-cis-retinoic acidC\C(\C=C\C12OC1(C)CCCC2(C)C)=C/C=C/C(/C)=C\C(O)=O2452.8Standard non polar33892256
5,6-Epoxy-13-cis-retinoic acidC\C(\C=C\C12OC1(C)CCCC2(C)C)=C/C=C/C(/C)=C\C(O)=O2591.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
5,6-Epoxy-13-cis-retinoic acid,1TMS,isomer #1CC(=C/C(=O)O[Si](C)(C)C)/C=C/C=C(C)/C=C/C12OC1(C)CCCC2(C)C2632.5Semi standard non polar33892256
5,6-Epoxy-13-cis-retinoic acid,1TBDMS,isomer #1CC(=C/C(=O)O[Si](C)(C)C(C)(C)C)/C=C/C=C(C)/C=C/C12OC1(C)CCCC2(C)C2846.7Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Epoxy-13-cis-retinoic 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 - 5,6-Epoxy-13-cis-retinoic acid 10V, Positive-QTOFsplash10-0002-0392000000-db71c362cf2ce5f0376b2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 20V, Positive-QTOFsplash10-0a4i-5890000000-8cda60e8ed359a4d31582019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 40V, Positive-QTOFsplash10-0pvi-9400000000-b652752049e9099c4c5f2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 10V, Negative-QTOFsplash10-014i-0089000000-db7b49ec35814d41b1462019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 20V, Negative-QTOFsplash10-01ba-0094000000-dc7fa9813bf0f44f3f222019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 40V, Negative-QTOFsplash10-053i-6960000000-b1133bf5dd927a284ac02019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 10V, Positive-QTOFsplash10-00rt-0192000000-861041c7dc974b088a422021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 20V, Positive-QTOFsplash10-0540-0590000000-4f77ff24993914b2af452021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 40V, Positive-QTOFsplash10-0gdu-7910000000-3b294bfc029780e1a3892021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 10V, Negative-QTOFsplash10-01b9-0198000000-91d1b99148247a6bd9812021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 20V, Negative-QTOFsplash10-00y0-0971000000-29094eb01d6c33d9ba2e2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Epoxy-13-cis-retinoic acid 40V, Negative-QTOFsplash10-066r-2932000000-86038457c94d4ed88c272021-09-24Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
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 IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound71316381
PDB IDNot Available
ChEBI IDNot Available
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. Samokyszyn VM, Marnett LJ: Hydroperoxide-dependent cooxidation of 13-cis-retinoic acid by prostaglandin H synthase. J Biol Chem. 1987 Oct 15;262(29):14119-33. [PubMed:3115987 ]