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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2019-07-23 05:44:33 UTC
HMDB IDHMDB0000857
Secondary Accession Numbers
  • HMDB00857
Metabolite Identification
Common NamePimelic acid
DescriptionPimelic acid is a group of compounds that are derivatives of heptanedioic acid with the general formula R-C7H11O4. Pimelic acid is the organic compound with the formula HO2C(CH2)5CO2H. Derivatives of pimelic acid are involved in the biosynthesis of the amino acid called lysine. Pimelic acid is one methylene longer than a related dicarboxylic acid, adipic acid, a precursor to many polyesters and polyamides. Pimelic acid has been synthesized from cyclohexanone and from salicylic acid.[1] In the former route, the additional carbon is suppled by dimethyloxalate, which reacts with the enolate. (Wikipedia).
Structure
Data?1563860673
Synonyms
ValueSource
1,5-Pentanedicarboxylic acidChEBI
6-Carboxyhexanoic acidChEBI
Heptanedioic acidChEBI
PimelateChEBI
6-CarboxyhexanoateKegg
1,5-PentanedicarboxylateGenerator
HeptanedioateGenerator
Acid, pimelicHMDB
Acids, pimelicHMDB
Pimelic acidsHMDB
1,7-HeptanedioateHMDB
1,7-Heptanedioic acidHMDB
HeptandioateHMDB
Heptandioic acidHMDB
Heptane-1,7-dioateHMDB
Heptane-1,7-dioic acidHMDB
PilerateHMDB
Pileric acidHMDB
Chemical FormulaC7H12O4
Average Molecular Weight160.1678
Monoisotopic Molecular Weight160.073558872
IUPAC Nameheptanedioic acid
Traditional Namepimelic acid
CAS Registry Number111-16-0
SMILES
OC(=O)CCCCCC(O)=O
InChI Identifier
InChI=1S/C7H12O4/c8-6(9)4-2-1-3-5-7(10)11/h1-5H2,(H,8,9)(H,10,11)
InChI KeyWLJVNTCWHIRURA-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
  • 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 Descriptors
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

Role

Industrial application:

Biological role:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point103 - 106 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility50 mg/mLNot Available
LogP0.61HANSCH,C ET AL. (1995)
Predicted Properties
PropertyValueSource
Water Solubility13.3 g/LALOGPS
logP0.51ALOGPS
logP0.94ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)4.05ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity37.34 m³·mol⁻¹ChemAxon
Polarizability16.31 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-056s-1910000000-58bf29a41b2e4b405df9JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0r7l-9100000000-aeff5d9828ac92b33028JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-054k-1910000000-fc6cb63b081b4f5f7fd3JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-056s-1910000000-58bf29a41b2e4b405df9JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-054k-1900000000-403538c5b4091abf0a3dJSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9400000000-3bc5f898da696375482fJSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00y0-9720000000-f599c8c7e2d374dc1d0cJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Negative (Annotated)splash10-0002-9300000000-a3d2b3924fcede41e331JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Negative (Annotated)splash10-0002-9100000000-7050dc1518d598ad5051JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Negative (Annotated)splash10-052e-9200000000-84550d0cfeb05e8d79bdJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - EI-B (Unknown) , Positivesplash10-0r7l-9100000000-b698134a5d1e523a961eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-0a4i-0900000000-a3b877a40a98e4d07993JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-0002-9500000000-6f90176eaadac29eae28JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-0002-9000000000-859f1028218d04c20dc6JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0002-9000000000-ef436118494b323530f4JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0002-9000000000-15fa4059d8c10e1e3a03JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0a4i-0900000000-a3b877a40a98e4d07993JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0002-9500000000-6f90176eaadac29eae28JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0002-9000000000-0ece97699a3ecbbd29c5JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0002-9000000000-aa9d7a3b0b034eb999acJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0002-9000000000-15fa4059d8c10e1e3a03JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03dl-1900000000-f72d396c48eae140d2eaJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-02tc-6900000000-148d1369a6cc8216a4d4JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0aou-9000000000-8148e8a28ecc0a5f1819JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0900000000-97c3b22812cb1495f92eJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a4i-2900000000-ec8e65ccb8032a2fffa0JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4l-9100000000-c8c106238d3a22f75dbcJSpectraViewer | MoNA
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
Biological Properties
Cellular Locations
  • Membrane
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.21 (0.11-0.31) uMInfant (0-1 year old)Not SpecifiedNormal details
FecesDetected but not Quantified Adult (>18 years old)BothNormal details
FecesDetected but not Quantified Not SpecifiedNot Specified
Normal
details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
UrineDetected and Quantified4.011 +/- 3.319 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal
    • Mordechai, Hien, ...
details
UrineDetected but not Quantified Adult (>18 years old)Both
Normal
details
UrineDetected and Quantified6.371 +/- 2.576 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal
    • Mordechai, Hien, ...
details
UrineDetected and Quantified15.8 +/- 2.4 umol/mmol creatinineChildren (1-13 years old)BothNormal details
UrineDetected and Quantified0.61-1.2 umol/mmol creatinineAdult (>18 years old)FemaleNormal details
UrineDetected but not Quantified Adult (>18 years old)Both
Normal
details
UrineDetected and Quantified2.4 (0.1-33.5) umol/mmol creatinineNewborn (0-30 days old)BothNormal details
UrineDetected and Quantified0.1 umol/mmol creatinineInfant (0-1 year old)BothNormal details
UrineDetected and Quantified2.2 (0.1-7.1) umol/mmol creatinineChildren (1-13 years old)Both
Normal
details
UrineDetected and Quantified3.6 (1.4-7.4) umol/mmol creatinineChildren (1-13 years old)Both
Normal
details
UrineDetected and Quantified2.2 (0.8-11.6) umol/mmol creatinineChildren (1-13 years old)Both
Normal
details
UrineDetected and Quantified2.2 (0.7-4.0) umol/mmol creatinineAdult (>18 years old)Both
Normal
details
UrineDetected and Quantified0.53-0.92 umol/mmol creatinineAdult (>18 years old)MaleNormal details
UrineDetected and Quantified1.9 (0.5-3.5) umol/mmol creatinineAdult (>18 years old)Both
Normal
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.68-12.7 uMInfant (0-1 year old)Female3-Hydroxydicarboxylic aciduria details
FecesDetected but not Quantified Adult (>18 years old)Both
Colorectal cancer
details
UrineDetected and Quantified2.507 +/- 2.054 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Mordechai, Hien, ...
details
UrineDetected and Quantified2.343 +/- 3.004 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Gastroesophageal reflux disease
    • Mordechai, Hien, ...
details
UrineDetected and Quantified7.664 +/- 7.255 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Mordechai, Hien, ...
details
UrineDetected and Quantified22.73 +/- 4.00 umol/mmol creatinineChildren (1-13 years old)BothMalnutrition (type kwashiorkor and marasmus) details
Associated Disorders and Diseases
Disease References
3-Hydroxydicarboxylic aciduria
  1. Hagenfeldt L, von Dobeln U, Holme E, Alm J, Brandberg G, Enocksson E, Lindeberg L: 3-Hydroxydicarboxylic aciduria--a fatty acid oxidation defect with severe prognosis. J Pediatr. 1990 Mar;116(3):387-92. [PubMed:2308028 ]
Colorectal cancer
  1. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Eosinophilic esophagitis
  1. (). Mordechai, Hien, and David S. Wishart. .
Associated OMIM IDs
DrugBank IDDB01856
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022283
KNApSAcK IDC00001199
Chemspider ID376
KEGG Compound IDC02656
BioCyc IDCPD-205
BiGG IDNot Available
Wikipedia LinkPimelic_acid
METLIN ID3280
PubChem Compound385
PDB IDNot Available
ChEBI ID30531
References
Synthesis ReferenceMurib, Jawad H.; Kahn, John H. Production of pimelic acid by carbonylation of e-caprolactone using excess water. U.S. (1989), 3 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Guneral F, Bachmann C: Age-related reference values for urinary organic acids in a healthy Turkish pediatric population. Clin Chem. 1994 Jun;40(6):862-6. [PubMed:8087979 ]
  2. Passi S, Picardo M, Mingrone G, Breathnach AS, Nazzaro-Porro M: Azelaic acid--biochemistry and metabolism. Acta Derm Venereol Suppl (Stockh). 1989;143:8-13. [PubMed:2505463 ]
  3. Pettit BR: The analysis of thiodiglycollic acid by selected ion monitoring. Clin Chim Acta. 1986 Apr 15;156(1):85-90. [PubMed:3698320 ]
  4. Niwa T, Ohki T, Maeda K, Saito A, Kobayashi K: Pattern of aliphatic dicarboxylic acids in uremic serum including a new organic acid, 2,4-dimethyladipic acid. Clin Chim Acta. 1979 Nov 15;99(1):71-83. [PubMed:498544 ]
  5. Mahadevappa VG, Holub BJ: The molecular species composition of individual diacyl phospholipids in human platelets. Biochim Biophys Acta. 1982 Oct 14;713(1):73-9. [PubMed:7138900 ]