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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2009-07-25 00:01:18 UTC
Update Date2022-03-07 02:51:26 UTC
HMDB IDHMDB0012476
Secondary Accession Numbers
  • HMDB12476
Metabolite Identification
Common Name(3S)-3-Hydroxydodec-cis-6-enoyl-CoA
Description(3S)-3-Hydroxydodec-cis-6-enoyl-CoA is an acyl-CoA with (3S)-3-hydroxydodec-cis-6-enoate moiety. An acyl-CoA (or formyl-CoA) is a coenzyme involved in the metabolism of fatty acids. It is a temporary compound formed when coenzyme A (CoA) attaches to the end of a long-chain fatty acid inside living cells. The compound undergoes beta oxidation, forming one or more molecules of acetyl-CoA. This, in turn, enters the citric acid cycle, eventually forming several molecules of ATP. (3S)-3-hydroxydodec-cis-6-enoyl-CoA is an intermediate in Di-unsaturated fatty acid beta-oxidation pathway. In the reaction, it acts as the precursor of producing (3S)-3-hydroxydodec-cis-6-enoyl-CoA[X].
Structure
Data?1582753059
Synonyms
ValueSource
(3S)-3-Hydroxy-6Z-dodecenoyl-CoAHMDB
(3S)-3-Hydroxy-6Z-dodecenoyl-coenzyme AHMDB
(3S)-3-Hydroxydodec-6Z-enoyl-CoAHMDB
(3S)-3-Hydroxydodec-6Z-enoyl-coenzyme AHMDB
3(S)-Hydroxy-cis-6-dodecenoyl-CoAHMDB
3(S)-Hydroxy-cis-6-dodecenoyl-coenzime aHMDB
3(S)-Hydroxy-cis-6-dodecenoyl-coenzyme AHMDB
4-({[({[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-hydroxydodec-6-enoyl)sulfanyl]ethyl}-C-hydroxycarbonimidoyl)ethyl]-3,3-dimethylbutanimidateHMDB
4-({[({[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-hydroxydodec-6-enoyl)sulphanyl]ethyl}-C-hydroxycarbonimidoyl)ethyl]-3,3-dimethylbutanimidateHMDB
4-({[({[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-hydroxydodec-6-enoyl)sulphanyl]ethyl}-C-hydroxycarbonimidoyl)ethyl]-3,3-dimethylbutanimidic acidHMDB
Chemical FormulaC33H56N7O18P3S
Average Molecular Weight963.82
Monoisotopic Molecular Weight963.261540159
IUPAC Name{[5-(6-amino-9H-purin-9-yl)-4-hydroxy-2-({[hydroxy({[hydroxy(3-hydroxy-3-{[2-({2-[(3-hydroxydodec-6-enoyl)sulfanyl]ethyl}carbamoyl)ethyl]carbamoyl}-2,2-dimethylpropoxy)phosphoryl]oxy})phosphoryl]oxy}methyl)oxolan-3-yl]oxy}phosphonic acid
Traditional Name[5-(6-aminopurin-9-yl)-4-hydroxy-2-({[hydroxy([hydroxy(3-hydroxy-3-{[2-({2-[(3-hydroxydodec-6-enoyl)sulfanyl]ethyl}carbamoyl)ethyl]carbamoyl}-2,2-dimethylpropoxy)phosphoryl]oxy)phosphoryl]oxy}methyl)oxolan-3-yl]oxyphosphonic acid
CAS Registry NumberNot Available
SMILES
CCCCCC=CCCC(O)CC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)N1C=NC2=C1N=CN=C2N
InChI Identifier
InChI=1S/C33H56N7O18P3S/c1-4-5-6-7-8-9-10-11-21(41)16-24(43)62-15-14-35-23(42)12-13-36-31(46)28(45)33(2,3)18-55-61(52,53)58-60(50,51)54-17-22-27(57-59(47,48)49)26(44)32(56-22)40-20-39-25-29(34)37-19-38-30(25)40/h8-9,19-22,26-28,32,41,44-45H,4-7,10-18H2,1-3H3,(H,35,42)(H,36,46)(H,50,51)(H,52,53)(H2,34,37,38)(H2,47,48,49)
InChI KeyXPCGRNRSXHPWGU-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 3-hydroxyacyl coas. These are organic compounds containing a 3-hydroxyl acylated coenzyme A derivative.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acyl thioesters
Direct Parent3-hydroxyacyl CoAs
Alternative Parents
Substituents
  • Coenzyme a or derivatives
  • Purine ribonucleoside 3',5'-bisphosphate
  • Purine ribonucleoside bisphosphate
  • Purine ribonucleoside diphosphate
  • Ribonucleoside 3'-phosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • 6-aminopurine
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Pentose monosaccharide
  • Purine
  • Imidazopyrimidine
  • Monoalkyl phosphate
  • Aminopyrimidine
  • Alkyl phosphate
  • Imidolactam
  • Organic phosphoric acid derivative
  • N-substituted imidazole
  • Monosaccharide
  • Pyrimidine
  • Phosphoric acid ester
  • Oxolane
  • Heteroaromatic compound
  • Azole
  • Imidazole
  • Carbothioic s-ester
  • Amino acid or derivatives
  • Thiocarboxylic acid ester
  • Secondary alcohol
  • Sulfenyl compound
  • Thiocarboxylic acid or derivatives
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organoheterocyclic compound
  • Azacycle
  • Carboximidic acid
  • Carboximidic acid derivative
  • Carboxylic acid derivative
  • Oxacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organic oxide
  • Carbonyl group
  • Primary amine
  • Alcohol
  • Hydrocarbon derivative
  • Organosulfur compound
  • Organooxygen compound
  • Amine
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
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 Solubility3.42 g/LALOGPS
logP0.8ALOGPS
logP-2.8ChemAxon
logS-2.6ALOGPS
pKa (Strongest Acidic)0.82ChemAxon
pKa (Strongest Basic)4.01ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count18ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area383.86 ŲChemAxon
Rotatable Bond Count29ChemAxon
Refractivity220.88 m³·mol⁻¹ChemAxon
Polarizability91.9 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+H]+249.34530932474
DeepCCS[M-H]-247.4530932474
DeepCCS[M-2H]-280.89330932474
DeepCCS[M+Na]+255.12330932474
AllCCS[M+H]+281.132859911
AllCCS[M+H-H2O]+281.732859911
AllCCS[M+NH4]+280.532859911
AllCCS[M+Na]+280.332859911
AllCCS[M-H]-285.532859911
AllCCS[M+Na-2H]-291.232859911
AllCCS[M+HCOO]-297.432859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.5.13 minutes32390414
Predicted by Siyang on May 30, 202212.0915 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20228.76 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid481.9 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid2009.3 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid153.9 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid138.7 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid169.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid120.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid447.5 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid506.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)1027.6 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid836.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid504.0 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid803.1 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid306.0 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid269.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate491.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA249.3 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water196.0 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (3S)-3-Hydroxydodec-cis-6-enoyl-CoA 10V, Positive-QTOFsplash10-000i-1912101103-9e38ed7a872e751126902019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (3S)-3-Hydroxydodec-cis-6-enoyl-CoA 20V, Positive-QTOFsplash10-000i-0921400000-ea93323078e5b7e08aca2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (3S)-3-Hydroxydodec-cis-6-enoyl-CoA 40V, Positive-QTOFsplash10-000i-1900100000-a399286896bd76347b742019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (3S)-3-Hydroxydodec-cis-6-enoyl-CoA 10V, Negative-QTOFsplash10-00o0-2911021304-347ba2421dfc11f6f91f2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (3S)-3-Hydroxydodec-cis-6-enoyl-CoA 20V, Negative-QTOFsplash10-001i-3901100001-70994810e3fa0d86bbf02019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (3S)-3-Hydroxydodec-cis-6-enoyl-CoA 40V, Negative-QTOFsplash10-057i-5900100000-8ece2c5e19e37f18977e2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (3S)-3-Hydroxydodec-cis-6-enoyl-CoA 10V, Positive-QTOFsplash10-01ot-0100000019-7b05559d096cc4a533f32021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (3S)-3-Hydroxydodec-cis-6-enoyl-CoA 20V, Positive-QTOFsplash10-002r-0500000079-c1145bbacd095110243a2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (3S)-3-Hydroxydodec-cis-6-enoyl-CoA 40V, Positive-QTOFsplash10-0a4i-0102900000-ae971327516f5de83a3f2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (3S)-3-Hydroxydodec-cis-6-enoyl-CoA 10V, Negative-QTOFsplash10-03di-0000000009-8fd23c0e6aa47427c3422021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (3S)-3-Hydroxydodec-cis-6-enoyl-CoA 20V, Negative-QTOFsplash10-03fu-3200101219-23e543aaa0a020c0d90f2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (3S)-3-Hydroxydodec-cis-6-enoyl-CoA 40V, Negative-QTOFsplash10-016v-4202501719-7d992abb1d066cd25b5f2021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • 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 IDFDB029086
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound76043724
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDCE2420
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. 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 ]
  3. 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 ]
  4. 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 ]
  5. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.