Showing metabocard for all-trans-5,6-Epoxyretinoic acid (BMDB0012451)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (2) Show 2 proteinsXML
Record Information
Version1.0
Creation Date2016-10-03 18:38:48 UTC
Update Date2020-05-21 16:29:27 UTC
BMDB IDBMDB0012451
Secondary Accession Numbers
  • BMDB12451
Metabolite Identification
Common Nameall-trans-5,6-Epoxyretinoic acid
Descriptionall-trans-5,6-Epoxyretinoic acid 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. all-trans-5,6-Epoxyretinoic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. all-trans-5,6-Epoxyretinoic acid can be biosynthesized from all-trans-retinoic acid; which is mediated by the enzyme cytochrome P450. In cattle, all-trans-All-trans-all-trans-5,6-epoxyretinoic acid is involved in the metabolic pathway called the retinol metabolism pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
all-trans-5,6-Epoxy-5,6-dihydroretinoic acidChEBI
all-trans-5,6-Epoxy-5,6-dihydroretinoateGenerator
all-trans-5,6-EpoxyretinoateGenerator
5,6-Epoxy-5,6-dihydro-retinoateHMDB
5,6-Epoxy-5,6-dihydro-retinoic acidHMDB
5,6-Epoxyretinoic acid, (13-cis)-isomerMeSH, HMDB
5,6-Epoxyretinoic acid, sodium saltMeSH, HMDB
5,6-Epoxyretinoic acidMeSH, HMDB
5,6-Epoxy-5,6-dihydroretinoic acidHMDB
5,6-Epoxy-atRAHMDB
all-trans-5,6-Epoxyretinoic acidHMDB
Chemical FormulaC20H28O3
Average Molecular Weight316.4345
Monoisotopic Molecular Weight316.203844762
IUPAC Name(2E,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(2E,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 Number13100-69-1
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-WEDZBJJJSA-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 Descriptors
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
  • Exogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cell membrane
  • Cytoplasm
  • Membrane
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted 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
Polarizability37.19 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0gb9-9174000000-06301725f04dbf9da5b0View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00di-9126000000-aaab7da3a75ae7d0ac69View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-066s-0394000000-5ab9d9f9a6f2942b53feView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4i-3490000000-ecf50862a1162e1b0ba8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9300000000-801580c3c0c49c76fd08View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-0179000000-815f6a20a086d254820bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01b9-1195000000-c470ae42b6bb7613d063View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-05a9-6960000000-e311a77eab0f7eeff493View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00rt-0192000000-861041c7dc974b088a42View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0540-0590000000-4f77ff24993914b2af45View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0gdu-7910000000-3b294bfc029780e1a389View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-01b9-0198000000-91d1b99148247a6bd981View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00y0-0971000000-29094eb01d6c33d9ba2eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-066r-2932000000-86038457c94d4ed88c27View in MoNA
Biological Properties
Cellular Locations
  • Cell membrane
  • Cytoplasm
  • Membrane
Biospecimen Locations
  • Kidney
  • Liver
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
KidneyExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
LiverExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
Abnormal Concentrations
Not Available
HMDB IDHMDB0012451
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB029067
KNApSAcK IDNot Available
Chemspider ID4515523
KEGG Compound IDC16680
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5363137
PDB IDNot Available
ChEBI ID80658
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Cytochrome P450 3A28
General function:
Secondary metabolites biosynthesis, transport and catabolism
Specific function:
Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.
Gene Name:
CYP3A28
Uniprot ID:
P79102
Molecular weight:
58152.0
Reactions
Retinoic acid → all-trans-5,6-Epoxyretinoic aciddetails
Enzyme Details
2. Cytochrome P450 2E1
General function:
Secondary metabolites biosynthesis, transport and catabolism
Specific function:
A cytochrome P450 monooxygenase involved in the metabolism of fatty acids. Mechanistically, uses molecular oxygen inserting one oxygen atom into a substrate, and reducing the second into a water molecule, with two electrons provided by NADPH via cytochrome P450 reductase (NADPH--hemoprotein reductase). Catalyzes the hydroxylation of carbon-hydrogen bonds. Hydroxylates fatty acids specifically at the omega-1 position displaying the highest catalytic activity for saturated fatty acids. May be involved in the oxidative metabolism of xenobiotics.
Gene Name:
CYP2E1
Uniprot ID:
O18963
Molecular weight:
56827.0
Reactions
Retinoic acid → all-trans-5,6-Epoxyretinoic aciddetails