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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2016-02-11 01:03:25 UTC
HMDB IDHMDB00857
Secondary Accession NumbersNone
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
Thumb
Synonyms
ValueSource
Heptanedioic acidKegg
6-CarboxyhexanoateKegg
HeptanedioateGenerator
PimelateGenerator
6-Carboxyhexanoic acidGenerator
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 KeyInChIKey=WLJVNTCWHIRURA-UHFFFAOYSA-N
Chemical Taxonomy
DescriptionThis compound 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
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Membrane
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point103 - 106 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility50.0 mg/mLNot Available
LogP0.61HANSCH,C ET AL. (1995)
Predicted Properties
PropertyValueSource
Water Solubility13.3 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity37.34 m3·mol-1ChemAxon
Polarizability16.31 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)splash10-056s-1910000000-58bf29a41b2e4b405df9View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Negative (Annotated)splash10-0002-9300000000-a3d2b3924fcede41e331View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Negative (Annotated)splash10-0002-9100000000-7050dc1518d598ad5051View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Negative (Annotated)splash10-052e-9200000000-84550d0cfeb05e8d79bdView in MoNA
LC-MS/MSLC-MS/MS Spectrum - EI-B (Unknown) , Positivesplash10-0r7l-9100000000-b698134a5d1e523a961eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-0a4i-0900000000-a3b877a40a98e4d07993View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-0002-9500000000-6f90176eaadac29eae28View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-0002-9000000000-859f1028218d04c20dc6View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0002-9000000000-ef436118494b323530f4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0002-9000000000-15fa4059d8c10e1e3a03View in MoNA
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
Biological Properties
Cellular Locations
  • Membrane
Biofluid Locations
  • Feces
  • Urine
Tissue LocationNot Available
PathwaysNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot ApplicableNot SpecifiedNot Specified
Normal
details
UrineDetected and Quantified4.011 +/- 3.319 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal
    • Mordechai, Hien, ...
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 but not QuantifiedNot ApplicableAdult (>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 (0.1-0.1) 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 Quantified1.9 (0.5-3.5) umol/mmol creatinineAdult (>18 years old)Both
Normal
details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
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 ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB022283
KNApSAcK IDNot Available
Chemspider ID376
KEGG Compound IDC02656
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPimelic acid
NuGOwiki LinkHMDB00857
Metagene LinkHMDB00857
METLIN ID3280
PubChem Compound385
PDB IDPML
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. [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. [2505463 ]
  3. Pettit BR: The analysis of thiodiglycollic acid by selected ion monitoring. Clin Chim Acta. 1986 Apr 15;156(1):85-90. [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. [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. [7138900 ]