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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2009-06-18 12:13:05 UTC
Update Date2021-09-14 15:46:22 UTC
HMDB IDHMDB0012451
Secondary Accession Numbers
  • HMDB0060093
  • HMDB12451
  • HMDB60093
Metabolite Identification
Common Nameall-trans-5,6-Epoxyretinoic acid
Descriptionall-trans-5,6-Epoxyretinoic acid, also known as 5,6-epoxy-atRA, is classified as a member of the retinoids. Retinoids 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 considered to be a practically insoluble (in water) and a weak acidic compound. all-trans-5,6-Epoxyretinoic acid is an isoprenoid lipid molecule. all-trans-5,6-Epoxyretinoic acid can be found primarily in human kidney and liver tissues; and in blood and urine. Within a cell, all-trans-5,6-epoxyretinoic acid is primarily located in the cytoplasm, in the extracellular space, or near the membrane.
Structure
Data?1582753056
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
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 Solubility0.0039 g/LALOGPS
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 RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+180.74831661259
DarkChem[M-H]-178.53531661259
DeepCCS[M-2H]-229.65130932474
DeepCCS[M+Na]+204.87830932474
AllCCS[M+H]+180.032859911
AllCCS[M+H-H2O]+177.032859911
AllCCS[M+NH4]+182.832859911
AllCCS[M+Na]+183.632859911
AllCCS[M-H]-185.632859911
AllCCS[M+Na-2H]-186.232859911
AllCCS[M+HCOO]-187.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
all-trans-5,6-Epoxyretinoic acidC\C(\C=C\C12OC1(C)CCCC2(C)C)=C/C=C/C(/C)=C/C(O)=O3855.1Standard polar33892256
all-trans-5,6-Epoxyretinoic acidC\C(\C=C\C12OC1(C)CCCC2(C)C)=C/C=C/C(/C)=C/C(O)=O2452.8Standard non polar33892256
all-trans-5,6-Epoxyretinoic 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
all-trans-5,6-Epoxyretinoic acid,1TMS,isomer #1CC(/C=C/C12OC1(C)CCCC2(C)C)=C\C=C\C(C)=C\C(=O)O[Si](C)(C)C2632.5Semi standard non polar33892256
all-trans-5,6-Epoxyretinoic acid,1TBDMS,isomer #1CC(/C=C/C12OC1(C)CCCC2(C)C)=C\C=C\C(C)=C\C(=O)O[Si](C)(C)C(C)(C)C2846.7Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - all-trans-5,6-Epoxyretinoic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-0gb9-9174000000-06301725f04dbf9da5b02017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - all-trans-5,6-Epoxyretinoic acid GC-MS (1 TMS) - 70eV, Positivesplash10-00di-9126000000-aaab7da3a75ae7d0ac692017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - all-trans-5,6-Epoxyretinoic 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 - all-trans-5,6-Epoxyretinoic acid 10V, Positive-QTOFsplash10-066s-0394000000-5ab9d9f9a6f2942b53fe2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-5,6-Epoxyretinoic acid 20V, Positive-QTOFsplash10-0a4i-3490000000-ecf50862a1162e1b0ba82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-5,6-Epoxyretinoic acid 40V, Positive-QTOFsplash10-0a4i-9300000000-801580c3c0c49c76fd082016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-5,6-Epoxyretinoic acid 10V, Negative-QTOFsplash10-014i-0179000000-815f6a20a086d254820b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-5,6-Epoxyretinoic acid 20V, Negative-QTOFsplash10-01b9-1195000000-c470ae42b6bb7613d0632016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-5,6-Epoxyretinoic acid 40V, Negative-QTOFsplash10-05a9-6960000000-e311a77eab0f7eeff4932016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-5,6-Epoxyretinoic acid 10V, Positive-QTOFsplash10-00rt-0192000000-861041c7dc974b088a422021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-5,6-Epoxyretinoic acid 20V, Positive-QTOFsplash10-0540-0590000000-4f77ff24993914b2af452021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-5,6-Epoxyretinoic acid 40V, Positive-QTOFsplash10-0gdu-7910000000-3b294bfc029780e1a3892021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-5,6-Epoxyretinoic acid 10V, Negative-QTOFsplash10-01b9-0198000000-91d1b99148247a6bd9812021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-5,6-Epoxyretinoic acid 20V, Negative-QTOFsplash10-00y0-0971000000-29094eb01d6c33d9ba2e2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-5,6-Epoxyretinoic acid 40V, Negative-QTOFsplash10-066r-2932000000-86038457c94d4ed88c272021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biospecimen Locations
  • Blood
  • Urine
Tissue Locations
  • Kidney
  • Liver
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableNormal
      Not Available
details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableNormal
      Not Available
details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
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
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. Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bolling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novere N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BO: A community-driven global reconstruction of human metabolism. Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. Epub 2013 Mar 3. [PubMed:23455439 ]
  2. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  3. 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 ]
  4. 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 ]
  5. 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 ]
  6. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.