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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-05-17 00:57:22 UTC
Update Date2022-03-07 03:17:44 UTC
HMDB IDHMDB0060373
Secondary Accession Numbers
  • HMDB60373
Metabolite Identification
Common Name3-Hydroxy-5-methylhex-4-enoyl-CoA
Description3-Hydroxy-5-methylhex-4-enoyl-CoA belongs to the class of organic compounds known as 3-hydroxy-3-alkylglutaryl coas. These are alpha, omega dicarboxyacyl-CoA that result from the formal condensation of the thiol group of coenzyme A with one of the carboxy groups of 3-hydroxy-3-alkylglutaric acid. 3-Hydroxy-5-methylhex-4-enoyl-CoA is a strong basic compound (based on its pKa).
Structure
Data?1563866051
SynonymsNot Available
Chemical FormulaC28H46N7O18P3S
Average Molecular Weight893.687
Monoisotopic Molecular Weight893.183287929
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-N-[2-({2-[(3-hydroxy-5-methylhex-4-enoyl)sulfanyl]ethyl}-C-hydroxycarbonimidoyl)ethyl]-3,3-dimethylbutanimidic 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-N-[2-({2-[(3-hydroxy-5-methylhex-4-enoyl)sulfanyl]ethyl}-C-hydroxycarbonimidoyl)ethyl]-3,3-dimethylbutanimidic 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/C28H46N7O18P3S/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/h9,13-14,16-17,21-23,27,36,39-40H,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)/t16?,17-,21-,22-,23+,27-/m1/s1
InChI KeyOLZYNLSKRKFUJC-FPVIQYCMSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 3-hydroxy-3-alkylglutaryl coas. These are alpha, omega dicarboxyacyl-CoA that result from the formal condensation of the thiol group of coenzyme A with one of the carboxy groups of 3-hydroxy-3-alkylglutaric acid.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acyl thioesters
Direct Parent3-hydroxy-3-alkylglutaryl CoAs
Alternative Parents
Substituents
  • Coenzyme a or derivatives
  • Purine ribonucleoside 3',5'-bisphosphate
  • Purine ribonucleoside bisphosphate
  • Purine ribonucleoside diphosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Ribonucleoside 3'-phosphate
  • Beta amino acid or derivatives
  • Glycosyl compound
  • N-glycosyl compound
  • Organic pyrophosphate
  • Monoterpenoid
  • Monosaccharide phosphate
  • Pentose monosaccharide
  • Aromatic monoterpenoid
  • Bicyclic monoterpenoid
  • 6-aminopurine
  • Medium-chain hydroxy acid
  • Imidazopyrimidine
  • Purine
  • Medium-chain fatty acid
  • Aminopyrimidine
  • Monoalkyl phosphate
  • Hydroxy fatty acid
  • Fatty acid
  • N-substituted imidazole
  • N-acyl-amine
  • Monosaccharide
  • Imidolactam
  • Fatty amide
  • Pyrimidine
  • Organic phosphoric acid derivative
  • Unsaturated fatty acid
  • Alkyl phosphate
  • Phosphoric acid ester
  • Imidazole
  • Tetrahydrofuran
  • Azole
  • Tertiary alcohol
  • Heteroaromatic compound
  • Amino acid or derivatives
  • Carbothioic s-ester
  • Thiocarboxylic acid ester
  • Secondary carboxylic acid amide
  • Carboxamide group
  • Secondary alcohol
  • Amino acid
  • Monocarboxylic acid or derivatives
  • Sulfenyl compound
  • Azacycle
  • Thiocarboxylic acid or derivatives
  • Organoheterocyclic compound
  • Oxacycle
  • Carboxylic acid derivative
  • Carboxylic acid
  • Organonitrogen compound
  • Organic nitrogen compound
  • Carbonyl group
  • Alcohol
  • Amine
  • Hydrocarbon derivative
  • Primary amine
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organosulfur compound
  • Organooxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
DispositionNot Available
ProcessNot Available
RoleNot 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 Solubility5.9 g/LALOGPS
logP-0.34ALOGPS
logP-5.7ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)0.82ChemAxon
pKa (Strongest Basic)4.94ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count20ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area390.84 ŲChemAxon
Rotatable Bond Count23ChemAxon
Refractivity198.44 m³·mol⁻¹ChemAxon
Polarizability82.96 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]-256.10730932474
DeepCCS[M+Na]+229.88330932474
AllCCS[M+H]+266.632859911
AllCCS[M+H-H2O]+267.132859911
AllCCS[M+NH4]+266.032859911
AllCCS[M+Na]+265.932859911
AllCCS[M-H]-263.432859911
AllCCS[M+Na-2H]-268.232859911
AllCCS[M+HCOO]-273.432859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-Hydroxy-5-methylhex-4-enoyl-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=C125534.7Standard polar33892256
3-Hydroxy-5-methylhex-4-enoyl-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=C124635.9Standard non polar33892256
3-Hydroxy-5-methylhex-4-enoyl-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=C126614.4Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-5-methylhex-4-enoyl-CoA 10V, Positive-QTOFsplash10-000i-1971000230-4c5f52c024360d518ac32017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-5-methylhex-4-enoyl-CoA 20V, Positive-QTOFsplash10-000i-1962000000-4dd998fbf2686c5584dd2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-5-methylhex-4-enoyl-CoA 40V, Positive-QTOFsplash10-000i-2940000000-aaa2d49c163252e745d82017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-5-methylhex-4-enoyl-CoA 10V, Negative-QTOFsplash10-00ai-5910131460-3ef1d776f8d4403006ac2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-5-methylhex-4-enoyl-CoA 20V, Negative-QTOFsplash10-003r-4901120010-8913558eb9066c1c66342017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-5-methylhex-4-enoyl-CoA 40V, Negative-QTOFsplash10-057i-4900100000-97ce1f0632d5fab8b1f52017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-5-methylhex-4-enoyl-CoA 10V, Positive-QTOFsplash10-0006-0000000190-8ad667059bb1e30855592021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-5-methylhex-4-enoyl-CoA 20V, Positive-QTOFsplash10-0a6u-1100000390-c34ec40644898f599e0a2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-5-methylhex-4-enoyl-CoA 40V, Positive-QTOFsplash10-000i-0019000000-55f893873b8a9a4288042021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-5-methylhex-4-enoyl-CoA 10V, Negative-QTOFsplash10-0006-0000000090-e57f501afa9572c158eb2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-5-methylhex-4-enoyl-CoA 20V, Negative-QTOFsplash10-00r6-5300003940-a4a0e1c97613803356312021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-5-methylhex-4-enoyl-CoA 40V, Negative-QTOFsplash10-0007-6403521900-3ba826bdd4f9610bf0942021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 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, 1000 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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C 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 IDC16469
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound9549330
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