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Record Information
StatusExpected but not Quantified
Creation Date2009-06-18 12:13:05 UTC
Update Date2019-07-09 15:15:25 UTC
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.
all-trans-5,6-Epoxy-5,6-dihydroretinoic acidChEBI
5,6-Epoxy-5,6-dihydro-retinoic acidHMDB
5,6-Epoxyretinoic acid, (13-cis)-isomerHMDB
5,6-Epoxyretinoic acid, sodium saltHMDB
5,6-Epoxyretinoic acidMeSH
5,6-Epoxy-5,6-dihydroretinoic acidHMDB
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
InChI Identifier
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
  • 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

Route of exposure:


Biological location:


Naturally occurring process:


Industrial application:

Biological role:

Physical Properties
Experimental Properties
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
Water Solubility0.0039 g/LALOGPS
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
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0gb9-9174000000-06301725f04dbf9da5b0JSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00di-9126000000-aaab7da3a75ae7d0ac69JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-066s-0394000000-5ab9d9f9a6f2942b53feJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4i-3490000000-ecf50862a1162e1b0ba8JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9300000000-801580c3c0c49c76fd08JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-0179000000-815f6a20a086d254820bJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01b9-1195000000-c470ae42b6bb7613d063JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-05a9-6960000000-e311a77eab0f7eeff493JSpectraViewer | MoNA
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biospecimen Locations
  • Blood
  • Urine
Tissue Locations
  • Kidney
  • Liver
Normal Concentrations
BloodExpected but not Quantified Not AvailableNot AvailableNormal
    UrineExpected but not Quantified Not AvailableNot AvailableNormal
      Abnormal Concentrations
      Not Available
      Associated Disorders and Diseases
      Disease ReferencesNone
      Associated OMIM IDsNone
      DrugBank IDNot Available
      Phenol Explorer Compound IDNot Available
      FoodDB 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
      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.