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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2007-05-22 17:57:51 UTC
Update Date2022-03-07 02:49:30 UTC
HMDB IDHMDB0006220
Secondary Accession Numbers
  • HMDB06220
Metabolite Identification
Common Name13-cis-Retinal
Description13-cis-Retinal is a naturally occurring retinoid. Retinoids are vitamin A analogs that have profound biological activities. Several retinoids have been reported to have antiinflammatory activity in certain animal models of arthritis, such as adjuvant-induced and streptococcal cell wall-induced arthritis in rats. Some retinoids also have been shown to possess antiinftammatory activity in man by their ability to modulate inflammatory diseases of the skin. It has been reported, for example, that retinoid treatment can inhibit neutrophil accumulation in cutaneous disorders such as psoriasis. (PMID:2123476 ).
Structure
Data?1582752375
Synonyms
ValueSource
(13cis)-RetinalChEBI
(2Z,4E,6E,8E)-3,7-Dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenalChEBI
13-cis-RetinaldehydeChEBI
RETINALChEBI
13Z-RetinalHMDB
cis-13-RetinalHMDB
Neoretinene aHMDB
Neovitamin a aldehydeHMDB
13-cis-RetinalMeSH, HMDB
Chemical FormulaC20H28O
Average Molecular Weight284.4357
Monoisotopic Molecular Weight284.214015518
IUPAC Name(2Z,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenal
Traditional Name13-cis retinal
CAS Registry Number472-86-6
SMILES
C\C(\C=C\C=C(/C)\C=C\C1=C(C)CCCC1(C)C)=C\C=O
InChI Identifier
InChI=1S/C20H28O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,15H,7,10,14H2,1-5H3/b9-6+,12-11+,16-8+,17-13-
InChI KeyNCYCYZXNIZJOKI-HWCYFHEPSA-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
  • Retinoid skeleton
  • Diterpenoid
  • Enal
  • Alpha,beta-unsaturated aldehyde
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aldehyde
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic 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 Solubility0.0042 g/LALOGPS
logP4.86ChemAxon
pKa (Strongest Basic)-4.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area17.07 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity96.87 m³·mol⁻¹ChemAxon
Polarizability35.47 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]+174.62431661259
DarkChem[M-H]-174.95931661259
DeepCCS[M+H]+189.36530932474
DeepCCS[M-H]-187.00730932474
DeepCCS[M-2H]-220.78330932474
DeepCCS[M+Na]+196.00930932474
AllCCS[M+H]+174.032859911
AllCCS[M+H-H2O]+170.732859911
AllCCS[M+NH4]+177.132859911
AllCCS[M+Na]+177.932859911
AllCCS[M-H]-178.332859911
AllCCS[M+Na-2H]-178.932859911
AllCCS[M+HCOO]-179.732859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
13-cis-RetinalC\C(\C=C\C=C(/C)\C=C\C1=C(C)CCCC1(C)C)=C\C=O3063.2Standard polar33892256
13-cis-RetinalC\C(\C=C\C=C(/C)\C=C\C1=C(C)CCCC1(C)C)=C\C=O2469.4Standard non polar33892256
13-cis-RetinalC\C(\C=C\C=C(/C)\C=C\C1=C(C)CCCC1(C)C)=C\C=O2398.5Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 13-cis-Retinal GC-MS (Non-derivatized) - 70eV, Positivesplash10-014i-2290000000-df9d2aa7545cc60a54f92017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 13-cis-Retinal GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 13-cis-Retinal 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 - 13-cis-Retinal 10V, Positive-QTOFsplash10-000i-0490000000-f543f08fbaf94a2e3f8e2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinal 20V, Positive-QTOFsplash10-000i-3940000000-83ca23fc3e32f84b7d9b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinal 40V, Positive-QTOFsplash10-0fri-9720000000-b077361f8a6c0a0a6c992016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinal 10V, Negative-QTOFsplash10-001i-0090000000-bad35938b77f181c29b92016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinal 20V, Negative-QTOFsplash10-001i-0090000000-1aadad0770df07f984362016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinal 40V, Negative-QTOFsplash10-00ko-4690000000-f624d342f88456375b9c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinal 10V, Negative-QTOFsplash10-0a59-0090000000-2ec2f8f314943441fa152021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinal 20V, Negative-QTOFsplash10-0pb9-0190000000-312cebb17ccd0189ab4d2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinal 40V, Negative-QTOFsplash10-000i-1590000000-b2551eac481c0c930a4d2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinal 10V, Positive-QTOFsplash10-00n3-1960000000-43f8c66f164764c373612021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinal 20V, Positive-QTOFsplash10-0609-3920000000-dbeab0a82b306761cf6a2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 13-cis-Retinal 40V, Positive-QTOFsplash10-052f-7900000000-d2bb7c1aeeb87d8833d22021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, CDCl3, experimental)2018-05-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • 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 IDFDB023844
KNApSAcK IDNot Available
Chemspider ID4940755
KEGG Compound IDNot Available
BioCyc IDCPD-13525
BiGG ID2455100
Wikipedia LinkRetinal
METLIN IDNot Available
PubChem Compound6436079
PDB IDNot Available
ChEBI ID45487
Food Biomarker OntologyNot Available
VMH IDRETINAL_CIS_13
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Hope WC, Patel BJ, Fiedler-Nagy C, Wittreich BH: Retinoids inhibit phospholipase A2 in human synovial fluid and arachidonic acid release from rat peritoneal macrophages. Inflammation. 1990 Oct;14(5):543-59. [PubMed:2123476 ]