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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-05-09 20:53:57 UTC
Update Date2022-03-07 03:17:38 UTC
HMDB IDHMDB0060092
Secondary Accession Numbers
  • HMDB60092
Metabolite Identification
Common Nameall-trans-3,4-Didehydroretinoate
Descriptionall-trans-3,4-Didehydroretinoate, also known as 3,4-didehydroretinoic acid or vitamin A2 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-3,4-Didehydroretinoate is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.
Structure
Data?1563866014
Synonyms
ValueSource
3,4-Didehydroretinoic acidChEBI
all-trans-3,4-Didehydro-retinoic acidChEBI
Didehydroretinoic acidChEBI
Vitamin a2 acidChEBI
3,4-DidehydroretinoateGenerator
all-trans-3,4-Didehydro-retinoateGenerator
DidehydroretinoateGenerator
all-trans-3,4-Didehydroretinoic acidGenerator
3,4-Didehydroretinoic acid, sodium saltHMDB
Chemical FormulaC20H26O2
Average Molecular Weight298.4192
Monoisotopic Molecular Weight298.193280076
IUPAC Name(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohexa-1,3-dien-1-yl)nona-2,4,6,8-tetraenoic acid
Traditional Name(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohexa-1,3-dien-1-yl)nona-2,4,6,8-tetraenoic acid
CAS Registry NumberNot Available
SMILES
C\C(\C=C\C1=C(C)C=CCC1(C)C)=C/C=C/C(/C)=C/C(O)=O
InChI Identifier
InChI=1S/C20H26O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6-12,14H,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8+,16-14+
InChI KeySYESMXTWOAQFET-YCNIQYBTSA-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
  • Methyl-branched fatty acid
  • Fatty acyl
  • Unsaturated fatty acid
  • Fatty acid
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organic oxide
  • Organic oxygen compound
  • Carbonyl group
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
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
Water Solubility0.0074 g/LALOGPS
logP6ALOGPS
logP4.65ChemAxon
logS-4.6ALOGPS
pKa (Strongest Acidic)5ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area37.3 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity98.91 m³·mol⁻¹ChemAxon
Polarizability35.72 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]+179.11931661259
DarkChem[M-H]-177.8931661259
DeepCCS[M+H]+198.07230932474
DeepCCS[M-H]-195.71430932474
DeepCCS[M-2H]-229.89930932474
DeepCCS[M+Na]+205.19630932474
AllCCS[M+H]+175.432859911
AllCCS[M+H-H2O]+172.132859911
AllCCS[M+NH4]+178.532859911
AllCCS[M+Na]+179.432859911
AllCCS[M-H]-178.032859911
AllCCS[M+Na-2H]-178.332859911
AllCCS[M+HCOO]-178.732859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
all-trans-3,4-DidehydroretinoateC\C(\C=C\C1=C(C)C=CCC1(C)C)=C/C=C/C(/C)=C/C(O)=O3810.3Standard polar33892256
all-trans-3,4-DidehydroretinoateC\C(\C=C\C1=C(C)C=CCC1(C)C)=C/C=C/C(/C)=C/C(O)=O2453.9Standard non polar33892256
all-trans-3,4-DidehydroretinoateC\C(\C=C\C1=C(C)C=CCC1(C)C)=C/C=C/C(/C)=C/C(O)=O2496.5Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
all-trans-3,4-Didehydroretinoate,1TMS,isomer #1CC1=C(/C=C/C(C)=C/C=C/C(C)=C/C(=O)O[Si](C)(C)C)C(C)(C)CC=C12701.7Semi standard non polar33892256
all-trans-3,4-Didehydroretinoate,1TBDMS,isomer #1CC1=C(/C=C/C(C)=C/C=C/C(C)=C/C(=O)O[Si](C)(C)C(C)(C)C)C(C)(C)CC=C12912.5Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - all-trans-3,4-Didehydroretinoate GC-MS (Non-derivatized) - 70eV, Positivesplash10-001i-2190000000-c6f9f2351a8952470f3b2017-09-20Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - all-trans-3,4-Didehydroretinoate GC-MS (1 TMS) - 70eV, Positivesplash10-0a4i-6259000000-3eef7c5898196604bf752017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - all-trans-3,4-Didehydroretinoate 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-3,4-Didehydroretinoate 10V, Positive-QTOFsplash10-001i-0290000000-bff7adf141bbcb7a77c52017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-3,4-Didehydroretinoate 20V, Positive-QTOFsplash10-0f80-2960000000-55281f0b8495de384ae02017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-3,4-Didehydroretinoate 40V, Positive-QTOFsplash10-059i-7900000000-0394e4380528d9fb243a2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-3,4-Didehydroretinoate 10V, Negative-QTOFsplash10-0f6t-0090000000-4ee06be0f46d388dee152017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-3,4-Didehydroretinoate 20V, Negative-QTOFsplash10-0ufs-0090000000-c5ee27afefaca27f48742017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - all-trans-3,4-Didehydroretinoate 40V, Negative-QTOFsplash10-0019-3490000000-3f59ab9cc9e6a95fef882017-10-06Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
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 Compound447276
PDB IDNot Available
ChEBI ID133794
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.