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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-10-09 21:00:55 UTC
HMDB IDHMDB0000857
Secondary Accession Numbers
  • HMDB00857
Metabolite Identification
Common NamePimelic acid
DescriptionPimelic acid, also known as heptanedioic acid is a dicarboxylic acid. 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 is essential for the synthesis of biotin (also called vitamin B7). Biotin is a heterocyclic, S-containing monocarboxylic acid that is made from two precursors, alanine and pimeloyl-CoA. Biotin is important in fatty acid synthesis, branched-chain amino acid catabolism, and gluconeogenesis. Biotin is found in a wide range of foods. Likewise, intestinal bacteria synthesize biotin, which is then absorbed by the host animal. Pimelic acid (which is the precursor for pimeloyl-CoA) is synthesized in many bacteria via a head-to-tail incorporation of acetate units through a modified fatty acid synthetic pathway using O-methyl esters disguised to resemble the canonical intermediates of the fatty acid synthetic pathway (PMID: 21435937 ). Some bacteria and yeast synthesize pimelic acid not by biosynthesis, but via cleavage of longer chain fatty acids (such as linolenic acid) via a cytochrome P450-like enzyme (PMID: 28196402 , 21435937 , 3236079 ). Pimelic acid is excreted in elevated amounts in the urine of individuals with mitochondrial beta-oxidation disorders and peroxisomal beta oxidation disorders (PMID: 1527989 )
Structure
Data?1582752160
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
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-1910000000-58bf29a41b2e4b405df9Spectrum
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0r7l-9100000000-aeff5d9828ac92b33028Spectrum
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-054k-1910000000-fc6cb63b081b4f5f7fd3Spectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-056s-1910000000-58bf29a41b2e4b405df9Spectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-054k-1900000000-403538c5b4091abf0a3dSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9400000000-3bc5f898da696375482fSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00y0-9720000000-f599c8c7e2d374dc1d0cSpectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Negative (Annotated)splash10-0002-9300000000-a3d2b3924fcede41e331Spectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Negative (Annotated)splash10-0002-9100000000-7050dc1518d598ad5051Spectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Negative (Annotated)splash10-052e-9200000000-84550d0cfeb05e8d79bdSpectrum
LC-MS/MSLC-MS/MS Spectrum - EI-B (Unknown) , Positivesplash10-0r7l-9100000000-b698134a5d1e523a961eSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-0a4i-0900000000-a3b877a40a98e4d07993Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-0002-9500000000-6f90176eaadac29eae28Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-0002-9000000000-859f1028218d04c20dc6Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0002-9000000000-ef436118494b323530f4Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0002-9000000000-15fa4059d8c10e1e3a03Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0a4i-0900000000-a3b877a40a98e4d07993Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0002-9500000000-6f90176eaadac29eae28Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0002-9000000000-0ece97699a3ecbbd29c5Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0002-9000000000-aa9d7a3b0b034eb999acSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0002-9000000000-15fa4059d8c10e1e3a03Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03dl-1900000000-f72d396c48eae140d2eaSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-02tc-6900000000-148d1369a6cc8216a4d4Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0aou-9000000000-8148e8a28ecc0a5f1819Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0900000000-97c3b22812cb1495f92eSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a4i-2900000000-ec8e65ccb8032a2fffa0Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4l-9100000000-c8c106238d3a22f75dbcSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableSpectrum
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 QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal
details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
FecesDetected but not QuantifiedNot QuantifiedAdult (>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 QuantifiedNot QuantifiedAdult (>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 QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
UrineDetected and Quantified0-1.3 umol/mmol creatinineInfant (0-1 year old)Male
Normal
details
UrineDetected and Quantified0-1.8 umol/mmol creatinineInfant (0-1 year old)Female
Normal
details
UrineDetected and Quantified0-2.0 umol/mmol creatinineInfant (0-1 year old)Male
Normal
details
UrineDetected and Quantified0-3.6 umol/mmol creatinineInfant (0-1 year old)Female
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 QuantifiedNot QuantifiedAdult (>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
FooDB 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
Food Biomarker OntologyNot Available
VMH IDPIME
MarkerDB IDMDB00000268
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 ]
  6. Cronan JE, Lin S: Synthesis of the alpha,omega-dicarboxylic acid precursor of biotin by the canonical fatty acid biosynthetic pathway. Curr Opin Chem Biol. 2011 Jun;15(3):407-13. doi: 10.1016/j.cbpa.2011.03.001. Epub 2011 Mar 23. [PubMed:21435937 ]
  7. Manandhar M, Cronan JE: Pimelic acid, the first precursor of the Bacillus subtilis biotin synthesis pathway, exists as the free acid and is assembled by fatty acid synthesis. Mol Microbiol. 2017 May;104(4):595-607. doi: 10.1111/mmi.13648. Epub 2017 Mar 3. [PubMed:28196402 ]
  8. Ohsugi M, Miyauchi K, Tachibana K, Nakao S: Formation of a biotin precursor, pimelic acid, in yeasts from C18 fatty acids. J Nutr Sci Vitaminol (Tokyo). 1988 Aug;34(4):343-52. doi: 10.3177/jnsv.34.343. [PubMed:3236079 ]
  9. Bennett MJ, Ragni MC, Hood I, Hale DE: Azelaic and pimelic acids: metabolic intermediates or artefacts? J Inherit Metab Dis. 1992;15(2):220-3. doi: 10.1007/BF01799635. [PubMed:1527989 ]