Hmdb loader
Survey
You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-05-17 00:59:43 UTC
Update Date2022-03-07 03:17:44 UTC
HMDB IDHMDB0060399
Secondary Accession Numbers
  • HMDB60399
Metabolite Identification
Common Name5-Methyl-3-oxo-4-hexenoyl-CoA
Description5-Methyl-3-oxo-4-hexenoyl-CoA belongs to the class of organic compounds known as pyrimidine ribonucleoside monophosphates. These are pyrimidine ribobucleotides with monophosphate group linked to the ribose moiety. 5-Methyl-3-oxo-4-hexenoyl-CoA is a strong basic compound (based on its pKa). These are organic compounds contaning a coenzyme A substructure linked to another moeity through an ester bond.
Structure
Data?1563866055
SynonymsNot Available
Chemical FormulaC28H44N7O18P3S
Average Molecular Weight891.671
Monoisotopic Molecular Weight891.167637865
IUPAC Name(2R)-4-({[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-2-hydroxy-3,3-dimethyl-N-[2-({2-[(5-methyl-3-oxohex-4-enoyl)sulfanyl]ethyl}-C-hydroxycarbonimidoyl)ethyl]butanimidic acid
Traditional Name(2R)-4-[({[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-2-hydroxy-3,3-dimethyl-N-[2-({2-[(5-methyl-3-oxohex-4-enoyl)sulfanyl]ethyl}-C-hydroxycarbonimidoyl)ethyl]butanimidic acid
CAS Registry NumberNot Available
SMILES
CC(C)=CC(=O)CC(=O)SCCN=C(O)CCN=C(O)[C@H](O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)N1C=NC2=C(N)N=CN=C12
InChI Identifier
InChI=1S/C28H44N7O18P3S/c1-15(2)9-16(36)10-19(38)57-8-7-30-18(37)5-6-31-26(41)23(40)28(3,4)12-50-56(47,48)53-55(45,46)49-11-17-22(52-54(42,43)44)21(39)27(51-17)35-14-34-20-24(29)32-13-33-25(20)35/h9,13-14,17,21-23,27,39-40H,5-8,10-12H2,1-4H3,(H,30,37)(H,31,41)(H,45,46)(H,47,48)(H2,29,32,33)(H2,42,43,44)/t17-,21-,22-,23+,27-/m1/s1
InChI KeyZFKZVSUJTDSJEY-SVHODSNWSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidine ribonucleoside monophosphates. These are pyrimidine ribobucleotides with monophosphate group linked to the ribose moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassPyrimidine ribonucleotides
Direct ParentPyrimidine ribonucleoside monophosphates
Alternative Parents
Substituents
  • Pyrimidine ribonucleoside monophosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Pentose monosaccharide
  • Halopyrimidine
  • Pyrimidone
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Aryl fluoride
  • Pyrimidine
  • Aryl halide
  • Phosphoric acid ester
  • Hydropyrimidine
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Vinylogous amide
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Urea
  • Secondary alcohol
  • 1,2-diol
  • Lactam
  • Azacycle
  • Organoheterocyclic compound
  • Oxacycle
  • Organopnictogen compound
  • Organooxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic oxygen compound
  • Organic nitrogen compound
  • Alcohol
  • Organonitrogen compound
  • Organohalogen compound
  • Organofluoride
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Not AvailableNot 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 Solubility5.71 g/LALOGPS
logP0.03ALOGPS
logP-2.7ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)0.82ChemAxon
pKa (Strongest Basic)4.79ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count20ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area387.68 ŲChemAxon
Rotatable Bond Count23ChemAxon
Refractivity197.75 m³·mol⁻¹ChemAxon
Polarizability81.37 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M-2H]-248.3930932474
DeepCCS[M+Na]+222.10230932474
AllCCS[M+H]+265.632859911
AllCCS[M+H-H2O]+266.132859911
AllCCS[M+NH4]+265.132859911
AllCCS[M+Na]+264.932859911
AllCCS[M-H]-262.632859911
AllCCS[M+Na-2H]-267.332859911
AllCCS[M+HCOO]-272.432859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5-Methyl-3-oxo-4-hexenoyl-CoACC(C)=CC(=O)CC(=O)SCCN=C(O)CCN=C(O)[C@H](O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)N1C=NC2=C(N)N=CN=C125853.7Standard polar33892256
5-Methyl-3-oxo-4-hexenoyl-CoACC(C)=CC(=O)CC(=O)SCCN=C(O)CCN=C(O)[C@H](O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)N1C=NC2=C(N)N=CN=C124769.9Standard non polar33892256
5-Methyl-3-oxo-4-hexenoyl-CoACC(C)=CC(=O)CC(=O)SCCN=C(O)CCN=C(O)[C@H](O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)N1C=NC2=C(N)N=CN=C126569.3Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-oxo-4-hexenoyl-CoA 10V, Positive-QTOFsplash10-0079-2981000220-d598b89c0cdbd7c89c662017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-oxo-4-hexenoyl-CoA 20V, Positive-QTOFsplash10-000i-1972000000-2cf5d30b326165b6e29c2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-oxo-4-hexenoyl-CoA 40V, Positive-QTOFsplash10-000i-2940000000-cb0f58122cb2fbdc3c8e2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-oxo-4-hexenoyl-CoA 10V, Negative-QTOFsplash10-00am-4910031350-44f75768bb5d6f6541cc2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-oxo-4-hexenoyl-CoA 20V, Negative-QTOFsplash10-001i-4900110010-a447720975d0c02d8e152017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-oxo-4-hexenoyl-CoA 40V, Negative-QTOFsplash10-057i-4900000000-752980c7dadc1cfcd1e02017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-oxo-4-hexenoyl-CoA 10V, Positive-QTOFsplash10-0006-0000000290-2e877744d8b00a89f5fa2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-oxo-4-hexenoyl-CoA 20V, Positive-QTOFsplash10-0536-3100001390-41e4f9e82dc1c11c34dd2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-oxo-4-hexenoyl-CoA 40V, Positive-QTOFsplash10-000i-0029000000-978028a7bcf4a1a1c93b2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-oxo-4-hexenoyl-CoA 10V, Negative-QTOFsplash10-0006-0000000090-0226b04a3dc5bff51fbd2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-oxo-4-hexenoyl-CoA 20V, Negative-QTOFsplash10-00dl-9300104780-1d9bd595d5eba8c2adf42021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-oxo-4-hexenoyl-CoA 40V, Negative-QTOFsplash10-002f-9301310400-2154d60d8217d68d65952021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
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 IDC16471
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound9549331
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. Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]
  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.

Enzymes

General function:
Involved in 3-hydroxyacyl-CoA dehydrogenase activity
Specific function:
Plays an essential role in the mitochondrial beta-oxidation of short chain fatty acids. Exerts it highest activity toward 3-hydroxybutyryl-CoA.
Gene Name:
HADH
Uniprot ID:
Q16836
Molecular weight:
36035.11
Reactions
3-Hydroxy-5-methylhex-4-enoyl-CoA + NAD → 5-Methyl-3-oxo-4-hexenoyl-CoA + NADH + Hydrogen Iondetails