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 Date2009-01-29 12:55:26 UTC
Update Date2022-03-07 02:51:12 UTC
HMDB IDHMDB0011604
Secondary Accession Numbers
  • HMDB11604
Metabolite Identification
Common Name4,8-Dimethylnonanoyl-CoA
Description4,8-Dimethylnonanoyl-CoA, also known as S-(4,8-dimethylnonanoate, belongs to the class of organic compounds known as 2,3,4-saturated fatty acyl coas. These are acyl-CoAs carrying a 2,3,4-saturated fatty acyl chain. 4,8-Dimethylnonanoyl-CoA is a strong basic compound (based on its pKa).
Structure
Data?1582752928
Synonyms
ValueSource
4(R)-8-Dimethyl-nonanoyl-CoAHMDB
4(R)-8-Dimethyl-nonanoyl-coenzyme AHMDB
S-(4,8-DimethylnonanoateHMDB
S-(4,8-Dimethylnonanoate)-CoAHMDB
S-(4,8-Dimethylnonanoate)-coenzyme AHMDB
S-(4,8-Dimethylnonanoic acidHMDB
Chemical FormulaC32H56N7O17P3S
Average Molecular Weight935.81
Monoisotopic Molecular Weight935.266623627
IUPAC Name{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-2-{[({[(3-{[2-({2-[(4,8-dimethylnonanoyl)sulfanyl]ethyl}carbamoyl)ethyl]carbamoyl}-3-hydroxy-2,2-dimethylpropoxy)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl)oxy]methyl}-4-hydroxyoxolan-3-yl]oxy}phosphonic acid
Traditional Name[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-2-({[(3-{[2-({2-[(4,8-dimethylnonanoyl)sulfanyl]ethyl}carbamoyl)ethyl]carbamoyl}-3-hydroxy-2,2-dimethylpropoxy(hydroxy)phosphoryl)oxy(hydroxy)phosphoryl]oxy}methyl)-4-hydroxyoxolan-3-yl]oxyphosphonic acid
CAS Registry Number204120-61-6
SMILES
CC(C)CCCC(C)CCC(=O)SCCNC(=O)CCNC(=O)C(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=C1N=CN=C2N
InChI Identifier
InChI=1S/C32H56N7O17P3S/c1-19(2)7-6-8-20(3)9-10-23(41)60-14-13-34-22(40)11-12-35-30(44)27(43)32(4,5)16-53-59(50,51)56-58(48,49)52-15-21-26(55-57(45,46)47)25(42)31(54-21)39-18-38-24-28(33)36-17-37-29(24)39/h17-21,25-27,31,42-43H,6-16H2,1-5H3,(H,34,40)(H,35,44)(H,48,49)(H,50,51)(H2,33,36,37)(H2,45,46,47)/t20?,21-,25-,26-,27?,31-/m1/s1
InChI KeyYGNKJFPEXQCWDB-DPSOZLMZSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 2,3,4-saturated fatty acyl coas. These are acyl-CoAs carrying a 2,3,4-saturated fatty acyl chain.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acyl thioesters
Direct Parent2,3,4-saturated fatty acyl 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
  • Beta amino acid or derivatives
  • Glycosyl compound
  • N-glycosyl compound
  • 6-aminopurine
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Pentose monosaccharide
  • Imidazopyrimidine
  • Purine
  • Monoalkyl phosphate
  • Aminopyrimidine
  • Imidolactam
  • N-acyl-amine
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Monosaccharide
  • Pyrimidine
  • Alkyl phosphate
  • Fatty amide
  • Phosphoric acid ester
  • Tetrahydrofuran
  • Imidazole
  • Azole
  • Heteroaromatic compound
  • Carbothioic s-ester
  • Secondary alcohol
  • Thiocarboxylic acid ester
  • Carboxamide group
  • Secondary carboxylic acid amide
  • Amino acid or derivatives
  • Sulfenyl compound
  • Thiocarboxylic acid or derivatives
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Carboxylic acid derivative
  • Organosulfur compound
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic nitrogen compound
  • Primary amine
  • Organopnictogen compound
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Amine
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Process
Role
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 Solubility2.89 g/LALOGPS
logP0.89ALOGPS
logP-3ChemAxon
logS-2.5ALOGPS
pKa (Strongest Acidic)0.83ChemAxon
pKa (Strongest Basic)4.95ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count17ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area363.63 ŲChemAxon
Rotatable Bond Count27ChemAxon
Refractivity213.54 m³·mol⁻¹ChemAxon
Polarizability88.69 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]+228.15330932474
DeepCCS[M-H]-226.49930932474
DeepCCS[M-2H]-260.69830932474
DeepCCS[M+Na]+234.3130932474
AllCCS[M+H]+279.232859911
AllCCS[M+H-H2O]+279.832859911
AllCCS[M+NH4]+278.732859911
AllCCS[M+Na]+278.532859911
AllCCS[M-H]-270.832859911
AllCCS[M+Na-2H]-276.432859911
AllCCS[M+HCOO]-282.432859911

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4,8-Dimethylnonanoyl-CoA 10V, Positive-QTOFsplash10-000i-1911101102-401444bc1fdff8215c592017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4,8-Dimethylnonanoyl-CoA 20V, Positive-QTOFsplash10-000i-0921300000-9fe1bff0176f97e27cc32017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4,8-Dimethylnonanoyl-CoA 40V, Positive-QTOFsplash10-000i-1900100000-58429b137a85673bc1c72017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4,8-Dimethylnonanoyl-CoA 10V, Negative-QTOFsplash10-00lr-2922031304-3dd5026989c5bc9cc1372017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4,8-Dimethylnonanoyl-CoA 20V, Negative-QTOFsplash10-00lr-3901110000-e197f4364788034ee4202017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4,8-Dimethylnonanoyl-CoA 40V, Negative-QTOFsplash10-057i-5900000000-7a6e179045da6101e3a12017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4,8-Dimethylnonanoyl-CoA 10V, Negative-QTOFsplash10-001i-0000000009-ac655bf23b80ff788dda2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4,8-Dimethylnonanoyl-CoA 20V, Negative-QTOFsplash10-00o0-3300202219-b61f2135a727d4c4d8942021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4,8-Dimethylnonanoyl-CoA 40V, Negative-QTOFsplash10-00p0-6104911834-955b72264f78a298ec4e2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4,8-Dimethylnonanoyl-CoA 10V, Positive-QTOFsplash10-000i-0000000019-6fbe3c457db3ba4a22e22021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4,8-Dimethylnonanoyl-CoA 20V, Positive-QTOFsplash10-000i-1500000192-6ec1dae6f052eed9cc692021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4,8-Dimethylnonanoyl-CoA 40V, Positive-QTOFsplash10-004i-0113900000-07c7535e4d2de57d3ae72021-09-24Wishart 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 IDFDB028315
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53481003
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. Verhoeven NM, Roe DS, Kok RM, Wanders RJ, Jakobs C, Roe CR: Phytanic acid and pristanic acid are oxidized by sequential peroxisomal and mitochondrial reactions in cultured fibroblasts. J Lipid Res. 1998 Jan;39(1):66-74. [PubMed:9469587 ]
  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 acyltransferase activity
Specific function:
Beta-oxidation of fatty acids. The highest activity concerns the C6 to C10 chain length substrate. Converts the end product of pristanic acid beta oxidation, 4,8-dimethylnonanoyl-CoA, to its corresponding carnitine ester.
Gene Name:
CROT
Uniprot ID:
Q9UKG9
Molecular weight:
10213.63
References
  1. Verhoeven NM, Roe DS, Kok RM, Wanders RJ, Jakobs C, Roe CR: Phytanic acid and pristanic acid are oxidized by sequential peroxisomal and mitochondrial reactions in cultured fibroblasts. J Lipid Res. 1998 Jan;39(1):66-74. [PubMed:9469587 ]