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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2009-07-25 00:09:00 UTC
Update Date2022-03-07 02:51:27 UTC
HMDB IDHMDB0012874
Secondary Accession Numbers
  • HMDB12874
Metabolite Identification
Common Name9,13-cis-Retinoic acid
Description9,13-cis-Retinoic 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. Retinoids (vitamin A and its analogs) are essential dietary substances that are needed by mammals for reproduction, normal embryogenesis, growth, vision, and maintaining normal cellular differentiation and the integrity of the immune system. Within cells, retinoids regulate gene transcription acting through ligand-dependent transcription factors, the retinoic acid receptors (RARs), and the retinoid X receptors (RXRs).
Structure
Data?1582753075
Synonyms
ValueSource
9,13-cis-RetinoateGenerator
3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexenyl)-(2E,4Z,6E,8Z)-nonatetraen-1-OateHMDB
3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexenyl)-(2E,4Z,6E,8Z)-nonatetraen-1-Oic acidHMDB
9,13-cis-Retinoic acidHMDB, Generator
9,13-cis-Retinoic acid anionHMDB
9,13-cis-Vitamin-a-acidHMDB
9,13-cis-Vitamin-alpha-acidHMDB
9,13-Di-cis-raHMDB
9-cis,13-cis-RetinoateHMDB
9-cis,13-cis-Retinoic acidHMDB
DcVAHMDB
9,13-Retinoic acidMeSH, HMDB
9,13-Di-cis-retinoateGenerator
Chemical FormulaC20H28O2
Average Molecular Weight300.4351
Monoisotopic Molecular Weight300.20893014
IUPAC Name(2Z,4E,6Z,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenoic acid
Traditional Name9,13-di-cis-retinoic acid
CAS Registry Number5352-74-9
SMILES
C\C(\C=C\C1=C(C)CCCC1(C)C)=C\C=C\C(\C)=C/C(O)=O
InChI Identifier
InChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8-,16-14-
InChI KeySHGAZHPCJJPHSC-CDMOMSTLSA-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
Process
Role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point181 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP6.30HANSCH,C ET AL. (1995)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.0048 g/LALOGPS
logP5.66ALOGPS
logP5.01ChemAxon
logS-4.8ALOGPS
pKa (Strongest Acidic)5ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area37.3 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity97.79 m³·mol⁻¹ChemAxon
Polarizability35.87 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+178.17231661259
DarkChem[M-H]-176.47931661259
DeepCCS[M+H]+200.44430932474
DeepCCS[M-H]-198.08630932474
DeepCCS[M-2H]-231.70130932474
DeepCCS[M+Na]+206.97830932474
AllCCS[M+H]+177.632859911
AllCCS[M+H-H2O]+174.432859911
AllCCS[M+NH4]+180.532859911
AllCCS[M+Na]+181.432859911
AllCCS[M-H]-181.132859911
AllCCS[M+Na-2H]-181.732859911
AllCCS[M+HCOO]-182.532859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
9,13-cis-Retinoic acidC\C(\C=C\C1=C(C)CCCC1(C)C)=C\C=C\C(\C)=C/C(O)=O3735.6Standard polar33892256
9,13-cis-Retinoic acidC\C(\C=C\C1=C(C)CCCC1(C)C)=C\C=C\C(\C)=C/C(O)=O2481.2Standard non polar33892256
9,13-cis-Retinoic acidC\C(\C=C\C1=C(C)CCCC1(C)C)=C\C=C\C(\C)=C/C(O)=O2553.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
9,13-cis-Retinoic acid,1TMS,isomer #1CC1=C(/C=C/C(C)=C\C=C\C(C)=C/C(=O)O[Si](C)(C)C)C(C)(C)CCC12701.4Semi standard non polar33892256
9,13-cis-Retinoic acid,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)CCC12906.6Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 9,13-cis-Retinoic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-000i-2190000000-86aaab132a5b092ebf102017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 9,13-cis-Retinoic acid GC-MS (1 TMS) - 70eV, Positivesplash10-0a4i-5139000000-29caedb85908ca2b99f42017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 9,13-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 - 9,13-cis-Retinoic acid 10V, Positive-QTOFsplash10-001i-0392000000-2208a551cdad109fbac32017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 20V, Positive-QTOFsplash10-053i-1940000000-ace2a3043044e52c8ad32017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 40V, Positive-QTOFsplash10-05nr-7900000000-1ee1af1ccb7ebac135f02017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 10V, Negative-QTOFsplash10-052b-0090000000-ca9b2a996cc511290cb52017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 20V, Negative-QTOFsplash10-0a5a-0090000000-4cb06190f795e58792082017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 40V, Negative-QTOFsplash10-053i-3590000000-09c02aaba9f83079f9c22017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 10V, Positive-QTOFsplash10-0zir-0973000000-3040e9e4a1a5448efbcb2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 20V, Positive-QTOFsplash10-060c-1950000000-f3b9c9b378f60b8c49a92021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 40V, Positive-QTOFsplash10-0ar3-5910000000-de22eb65f274483f3f982021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 10V, Negative-QTOFsplash10-052b-0090000000-5f942e3b870e7bd0121b2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 20V, Negative-QTOFsplash10-0a4i-0190000000-22b445382d39772800452021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9,13-cis-Retinoic acid 40V, Negative-QTOFsplash10-016r-4900000000-0005b37f6d54a42a84f62021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
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 IDFDB029194
KNApSAcK IDNot Available
Chemspider ID4925342
KEGG Compound IDC00777
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound6419708
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. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. 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 ]
  3. 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 ]
  4. 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 ]
  5. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.