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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2007-05-22 17:52:59 UTC
Update Date2022-09-22 18:34:19 UTC
HMDB IDHMDB0006218
Secondary Accession Numbers
  • HMDB06218
Metabolite Identification
Common Name9-cis-Retinal
DescriptionIn vivo, 9-cis-retinal is formed through oxidation of 9-cis-retinol by cis-retinol dehydrogenase (cRDH). (PMID:15572038 ). The generation of retinoic acid from retinol is a two-step reaction, with the rate-limiting step being the oxidation of retinol into the intermediate retinaldehyde. Two classes of. unrelated enzymes have been implicated in the oxidation of retinol, the classical cytosolic medium chain alcohol dehydrogenases and recently identified microsomal members of the short chain alcohol dehydrogenase reductase (SDR) superfamily. Further oxidation of the retinaldehyde to the retinoic acid is believed to be catalyzed by several cytosolic aldehyde dehydrogenases. Retinoids are micronutrients required to maintain and promote health of vertebrates. They act physiologically by participating in the visual cycle, in regulating cell differentiation, in embryonic development (PMID:10893430 ), in maintaining normal reproduction, and in the immune response (PMID:8882153 ). In non-ocular tissues, the effects of retinoids within the body are mediated through retinoic acid receptors (RARs) and retinoid X receptors (RXRs), which act to regulate gene expression as ligand-dependent transcription factors. The naturally occurring ligands for these nuclear receptors are thought to be all-trans-retinoic acid for RARs and 9-cis-retinoic acid for RXRs (PMID:10322133 ). While many details of the molecular actions of the RARs and RXRs in regulating gene transcription are understood (PMID:10418975 ), tissue-specific synthetic pathway(s) of their ligands has not been adequately defined. Nevertheless, the therapeutic efficacy of retinoids, including 9-cis-retinoic acid, is well established in both tissue culture and animal models of breast cancer (PMID:8825126 , PMID:12743994 ).
Structure
Data?1582752375
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
Physiological effectNot Available
Disposition
Process
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 Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M+H]+MetCCS_train_pos170.13530932474
[M+H]+Not Available170.471http://allccs.zhulab.cn/database/detail?ID=AllCCS00000455
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.0042 g/LALOGPS
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 RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+173.93831661259
DarkChem[M-H]-174.20231661259
DeepCCS[M+H]+181.62230932474
DeepCCS[M-H]-179.26430932474
DeepCCS[M-2H]-212.96330932474
DeepCCS[M+Na]+188.18930932474
AllCCS[M+H]+174.532859911
AllCCS[M+H-H2O]+171.332859911
AllCCS[M+NH4]+177.532859911
AllCCS[M+Na]+178.432859911
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
9-cis-RetinalC/C(/C=C/C=C(/C)\C=C\C1=C(C)CCCC1(C)C)=C\C=O3063.2Standard polar33892256
9-cis-RetinalC/C(/C=C/C=C(/C)\C=C\C1=C(C)CCCC1(C)C)=C\C=O2469.4Standard non polar33892256
9-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 - 9-cis-Retinal GC-MS (Non-derivatized) - 70eV, Positivesplash10-014i-2290000000-df9d2aa7545cc60a54f92017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 9-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 - 9-cis-Retinal 10V, Positive-QTOFsplash10-000i-1490000000-97cddfba9819c34173862017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinal 20V, Positive-QTOFsplash10-001s-3920000000-0be8a19c3cba33e3b06b2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinal 40V, Positive-QTOFsplash10-0kui-9720000000-a579102a9f5600032e3f2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinal 10V, Negative-QTOFsplash10-001i-0090000000-e7d5d678e91ec531c2ae2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinal 20V, Negative-QTOFsplash10-0a59-0090000000-8af2668c966a1c8a3cef2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinal 40V, Negative-QTOFsplash10-00ku-3690000000-54506b9021b67caed0412017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinal 10V, Positive-QTOFsplash10-00n3-1960000000-43f8c66f164764c373612021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinal 20V, Positive-QTOFsplash10-0609-3920000000-dbeab0a82b306761cf6a2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinal 40V, Positive-QTOFsplash10-052f-7900000000-d2bb7c1aeeb87d8833d22021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinal 10V, Negative-QTOFsplash10-0a59-0090000000-2ec2f8f314943441fa152021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinal 20V, Negative-QTOFsplash10-0pb9-0190000000-312cebb17ccd0189ab4d2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-cis-Retinal 40V, Negative-QTOFsplash10-000i-1590000000-b2551eac481c0c930a4d2021-09-23Wishart 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 Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
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
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
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 References
  1. Paik J, Blaner WS, Swisshelm K: Cis-retinol dehydrogenase: 9-cis-retinol metabolism and its effect on proliferation of human MCF7 breast cancer cells. Exp Cell Res. 2005 Feb 1;303(1):183-96. [PubMed:15572038 ]
  2. Ross SA, McCaffery PJ, Drager UC, De Luca LM: Retinoids in embryonal development. Physiol Rev. 2000 Jul;80(3):1021-54. [PubMed:10893430 ]
  3. Glass CK: Some new twists in the regulation of gene expression by thyroid hormone and retinoic acid receptors. J Endocrinol. 1996 Sep;150(3):349-57. [PubMed:8882153 ]
  4. Xu L, Glass CK, Rosenfeld MG: Coactivator and corepressor complexes in nuclear receptor function. Curr Opin Genet Dev. 1999 Apr;9(2):140-7. [PubMed:10322133 ]
  5. McKenna NJ, Xu J, Nawaz Z, Tsai SY, Tsai MJ, O'Malley BW: Nuclear receptor coactivators: multiple enzymes, multiple complexes, multiple functions. J Steroid Biochem Mol Biol. 1999 Apr-Jun;69(1-6):3-12. [PubMed:10418975 ]
  6. Gottardis MM, Lamph WW, Shalinsky DR, Wellstein A, Heyman RA: The efficacy of 9-cis retinoic acid in experimental models of cancer. Breast Cancer Res Treat. 1996;38(1):85-96. [PubMed:8825126 ]
  7. Paik J, Blaner WS, Sommer KM, Moe R, Swisshlem K: Retinoids, retinoic acid receptors, and breast cancer. Cancer Invest. 2003 Apr;21(2):304-12. [PubMed:12743994 ]

Only showing the first 10 proteins. There are 11 proteins in total.

Enzymes

General function:
Involved in oxidoreductase activity
Specific function:
Binds free retinal and cellular retinol-binding protein-bound retinal. Can convert/oxidize retinaldehyde to retinoic acid (By similarity).
Gene Name:
ALDH1A1
Uniprot ID:
P00352
Molecular weight:
54861.44
Reactions
9-cis-Retinal + NAD + Water → 9-cis-Retinoic acid + NADH + Hydrogen Iondetails
General function:
Involved in oxidoreductase activity
Specific function:
Recognizes as substrates free retinal and cellular retinol-binding protein-bound retinal. Does metabolize octanal and decanal but does not metabolize citral, benzaldehyde, acetaldehyde and propanal efficiently (By similarity).
Gene Name:
ALDH1A2
Uniprot ID:
O94788
Molecular weight:
54672.24
Reactions
9-cis-Retinal + NAD + Water → 9-cis-Retinoic acid + NADH + Hydrogen Iondetails
General function:
Involved in zinc ion binding
Specific function:
Class-III ADH is remarkably ineffective in oxidizing ethanol, but it readily catalyzes the oxidation of long-chain primary alcohols and the oxidation of S-(hydroxymethyl) glutathione.
Gene Name:
ADH5
Uniprot ID:
P11766
Molecular weight:
39723.945
General function:
Involved in zinc ion binding
Specific function:
Not Available
Gene Name:
ADH1B
Uniprot ID:
P00325
Molecular weight:
39835.17
General function:
Involved in zinc ion binding
Specific function:
Could function in retinol oxidation for the synthesis of retinoic acid, a hormone important for cellular differentiation. Medium-chain (octanol) and aromatic (m-nitrobenzaldehyde) compounds are the best substrates. Ethanol is not a good substrate but at the high ethanol concentrations reached in the digestive tract, it plays a role in the ethanol oxidation and contributes to the first pass ethanol metabolism.
Gene Name:
ADH7
Uniprot ID:
P40394
Molecular weight:
41480.985
General function:
Involved in zinc ion binding
Specific function:
Not Available
Gene Name:
ADH1A
Uniprot ID:
P07327
Molecular weight:
39858.37
General function:
Involved in zinc ion binding
Specific function:
Not Available
Gene Name:
ADH6
Uniprot ID:
P28332
Molecular weight:
39072.275
General function:
Involved in zinc ion binding
Specific function:
Not Available
Gene Name:
ADH1C
Uniprot ID:
P00326
Molecular weight:
39867.27
General function:
Secondary metabolites biosynthesis, transport and catabolism
Specific function:
Symmetrically cleaves beta-carotene into two molecules of retinal. The reaction proceeds in three stages, epoxidation of the 15,15'-double bond, hydration of the double bond leading to ring opening, and oxidative cleavage of the diol formed.
Gene Name:
BCMO1
Uniprot ID:
Q9HAY6
Molecular weight:
62636.69
General function:
Involved in oxidoreductase activity
Specific function:
Converts 9-cis-retinal to 9-cis-retinoic acid. Has lower activity towards 13-cis-retinal. Has much lower activity towards all-trans-retinal. Has highest activity with benzaldehyde and decanal (in vitro). Has a preference for NAD, but shows considerable activity with NADP (in vitro)
Gene Name:
ALDH8A1
Uniprot ID:
Q9H2A2
Molecular weight:
53400.9

Only showing the first 10 proteins. There are 11 proteins in total.