Showing metabocard for 9-cis-Retinal (BMDB0006218)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (2) Show 2 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 23:20:28 UTC
Update Date2020-05-21 16:29:06 UTC
BMDB IDBMDB0006218
Secondary Accession Numbers
  • BMDB06218
Metabolite Identification
Common Name9-cis-Retinal
Description13-cis-13-cis-13-cis-retinal, also known as 13Z-13-cis-retinal or 13-cis-retinal, 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. Thus, 13-cis-13-cis-retinal is considered to be an isoprenoid lipid molecule. 13-cis-13-cis-13-cis-retinal is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. 13-cis-13-cis-13-cis-retinal exists in all living organisms, ranging from bacteria to humans. In cattle, 13-cis-13-cis-retinal is involved in the metabolic pathway called the retinol metabolism pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
(2E,4E,6Z,8E)-3,7-Dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenalChEBI
(9cis)-RetinalChEBI
9-C-RetinalChEBI
9-cis-3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenalChEBI
9-cis-7,11,13-trans-RetinalChEBI
9-cis-RetinaldehydeChEBI
9-cis-Vitamin a aldehydeChEBI
Isoretinene aChEBI
cis-9-RetinalHMDB
Chemical FormulaC20H28O
Average Molecular Weight284.4357
Monoisotopic Molecular Weight284.214015518
IUPAC Name(2E,4E,6Z,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenal
Traditional Name9-cis-retinal
CAS Registry Number514-85-2
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-MKOSUFFBSA-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
StatusExpected but not Quantified
Origin
  • Endogenous
  • Exogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cell membrane
  • Cytoplasm
  • Membrane
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP6.62ALOGPS
logP4.86ChemAxon
logS-4.8ALOGPS
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
Polarizability34.99 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-014i-2290000000-df9d2aa7545cc60a54f9View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-1490000000-97cddfba9819c3417386View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001s-3920000000-0be8a19c3cba33e3b06bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0kui-9720000000-a579102a9f5600032e3fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-0090000000-e7d5d678e91ec531c2aeView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a59-0090000000-8af2668c966a1c8a3cefView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00ku-3690000000-54506b9021b67caed041View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00n3-1960000000-43f8c66f164764c37361View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0609-3920000000-dbeab0a82b306761cf6aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-052f-7900000000-d2bb7c1aeeb87d8833d2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a59-0090000000-2ec2f8f314943441fa15View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0pb9-0190000000-312cebb17ccd0189ab4dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-000i-1590000000-b2551eac481c0c930a4dView in MoNA
1D NMR1H NMR Spectrum (1D, 600 MHz, CDCl3, experimental)Not AvailableView in JSpectraViewer
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, CDCl3, experimental)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cell membrane
  • Cytoplasm
  • Membrane
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0006218
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023842
KNApSAcK IDNot Available
Chemspider ID4940758
KEGG Compound IDC16681
BioCyc IDCPD-13536
BiGG ID2265509
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound6436082
PDB IDNot Available
ChEBI ID78273
References
Synthesis ReferenceOstapenko, I. A.; Furaev, V. V. The 9-cis isomerization of all-trans-retinal during in vitro regeneration of visual pigment. Nature (London), New Biology (1973), 243(127), 185-6.
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Retinal dehydrogenase 1
General function:
Energy production and conversion
Specific function:
Can convert/oxidize retinaldehyde to retinoic acid. Binds free retinal and cellular retinol-binding protein-bound retinal. May have a broader specificity and oxidize other aldehydes in vivo.
Gene Name:
ALDH1A1
Uniprot ID:
P48644
Molecular weight:
54806.0
Reactions
9-cis-Retinal + NAD + Water → 9-cis-Retinoic acid + NADHdetails
Enzyme Details
2. Retinol dehydrogenase 12
General function:
Lipid transport and metabolism
Specific function:
Retinoids dehydrogenase/reductase with a clear preference for NADP. Displays high activity towards 9-cis, 11-cis and all-trans-retinal. Shows very weak activity towards 13-cis-retinol. Also exhibits activity, albeit with lower affinity than for retinaldehydes, towards lipid peroxidation products (C9 aldehydes) such as 4-hydroxynonenal and trans-2-nonenal. May play an important function in photoreceptor cells to detoxify 4-hydroxynonenal and potentially other toxic aldehyde products resulting from lipid peroxidation. Has no dehydrogenase activity towards steroids.
Gene Name:
RDH12
Uniprot ID:
P59837
Molecular weight:
35171.0
Reactions
9-cis-Retinol + NADP → 9-cis-Retinal + NADPHdetails