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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2013-02-26 19:02:29 UTC
Update Date2023-02-21 17:29:21 UTC
HMDB IDHMDB0059757
Secondary Accession Numbers
  • HMDB59757
Metabolite Identification
Common Name3-Methylpimelic acid
Description3-Methylpimelic acid, also known as 3-methylpimelate, belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms. 3-Methylpimelic acid is a weakly acidic compound (based on its pKa).
Structure
Data?1677000560
Synonyms
ValueSource
3-MethylpimelateGenerator
3-MethylheptanedioateGenerator
Chemical FormulaC8H14O4
Average Molecular Weight174.1944
Monoisotopic Molecular Weight174.089208936
IUPAC Name3-methylheptanedioic acid
Traditional Name3-methylheptanedioic acid
CAS Registry Number10200-31-4
SMILES
CC(CCCC(O)=O)CC(O)=O
InChI Identifier
InChI=1S/C8H14O4/c1-6(5-8(11)12)3-2-4-7(9)10/h6H,2-5H2,1H3,(H,9,10)(H,11,12)
InChI KeyNXDCNRPLRGMKHU-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentMedium-chain fatty acids
Alternative Parents
Substituents
  • Medium-chain fatty acid
  • Methyl-branched fatty acid
  • Branched fatty acid
  • Dicarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
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 Solubility6.07 g/LALOGPS
logP0.89ALOGPS
logP1.22ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)4.15ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity41.89 m³·mol⁻¹ChemAxon
Polarizability17.95 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+140.30331661259
DarkChem[M-H]-135.46931661259
DeepCCS[M+H]+133.34430932474
DeepCCS[M-H]-129.51230932474
DeepCCS[M-2H]-166.72830932474
DeepCCS[M+Na]+142.11730932474
AllCCS[M+H]+140.832859911
AllCCS[M+H-H2O]+137.032859911
AllCCS[M+NH4]+144.432859911
AllCCS[M+Na]+145.432859911
AllCCS[M-H]-139.432859911
AllCCS[M+Na-2H]-141.032859911
AllCCS[M+HCOO]-142.932859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-Methylpimelic acidCC(CCCC(O)=O)CC(O)=O2436.7Standard polar33892256
3-Methylpimelic acidCC(CCCC(O)=O)CC(O)=O1248.0Standard non polar33892256
3-Methylpimelic acidCC(CCCC(O)=O)CC(O)=O1505.8Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3-Methylpimelic acid,1TMS,isomer #1CC(CCCC(=O)O[Si](C)(C)C)CC(=O)O1541.4Semi standard non polar33892256
3-Methylpimelic acid,1TMS,isomer #2CC(CCCC(=O)O)CC(=O)O[Si](C)(C)C1540.8Semi standard non polar33892256
3-Methylpimelic acid,2TMS,isomer #1CC(CCCC(=O)O[Si](C)(C)C)CC(=O)O[Si](C)(C)C1629.4Semi standard non polar33892256
3-Methylpimelic acid,1TBDMS,isomer #1CC(CCCC(=O)O[Si](C)(C)C(C)(C)C)CC(=O)O1783.6Semi standard non polar33892256
3-Methylpimelic acid,1TBDMS,isomer #2CC(CCCC(=O)O)CC(=O)O[Si](C)(C)C(C)(C)C1784.9Semi standard non polar33892256
3-Methylpimelic acid,2TBDMS,isomer #1CC(CCCC(=O)O[Si](C)(C)C(C)(C)C)CC(=O)O[Si](C)(C)C(C)(C)C2077.2Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-Methylpimelic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-02bf-9800000000-848b0992d7c8e32d78b12017-09-20Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Methylpimelic acid GC-MS (2 TMS) - 70eV, Positivesplash10-0079-9331000000-306b42766798d5497f0e2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Methylpimelic acid 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 - 3-Methylpimelic acid 10V, Positive-QTOFsplash10-0a4i-0900000000-df18c01c6fb1893f682c2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylpimelic acid 20V, Positive-QTOFsplash10-0691-6900000000-2a24bb693567948ed7712017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylpimelic acid 40V, Positive-QTOFsplash10-014i-9000000000-d88d3fc86ff2fcfbd88a2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylpimelic acid 10V, Negative-QTOFsplash10-05i0-0900000000-c89e08dcb101966b611b2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylpimelic acid 20V, Negative-QTOFsplash10-0adi-1900000000-8e6c87f4a1d7ad6c89b32017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylpimelic acid 40V, Negative-QTOFsplash10-0a4i-9500000000-d7012b2fd187ef59da742017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylpimelic acid 10V, Negative-QTOFsplash10-024i-0900000000-eadd6b91fe3648187b7f2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylpimelic acid 20V, Negative-QTOFsplash10-0a6r-5900000000-7325d07601c0ddfb88532021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylpimelic acid 40V, Negative-QTOFsplash10-0a4l-9100000000-268318fd7fc1150c897d2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylpimelic acid 10V, Positive-QTOFsplash10-014i-7900000000-a1fe9a32f919a2521b032021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylpimelic acid 20V, Positive-QTOFsplash10-00lr-9200000000-681fa1dc90e8b4f3a8542021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylpimelic acid 40V, Positive-QTOFsplash10-00kf-9000000000-527c018476f3935938e12021-09-24Wishart 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

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-04FELIX labView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
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 IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound21510350
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. 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.