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
Version4.0
Creation Date2007-04-12 18:42:28 UTC
Update Date2017-09-27 08:24:39 UTC
HMDB IDHMDB0005960
Secondary Accession Numbers
  • HMDB05960
Metabolite Identification
Common NameD-Pipecolic acid
DescriptionD-Pipecolic acid is a normal human metabolite found in human biofluids. Normal adults excrete pipecolic acid primarily as the D-enantiomer even though it is present in the blood stream mainly as the L-enantiomer. It is believed that D-Pipecolic acid originates from the metabolism of intestinal bacteria and from dietary sources. High levels of D-Pipecolic acid are not found in plasma, but they are increased in urine of patients with chronic liver disease. (PMID: 6501504 , 6490790 , 11719476 , 8398594 ).
Structure
Thumb
Synonyms
ValueSource
(R)-Pipecolic acidChEBI
(R)-Piperidine-2-carboxylic acidChEBI
6-CARBOXYPIPERIDINEChEBI
(R)-PipecolateGenerator
D-PipecolateGenerator
(R)-Piperidine-2-carboxylateGenerator
(+)-Pipecolic acidHMDB
(+)-Pipecolinic acidHMDB
(2R)-2-Piperidinecarboxylic acidHMDB
(2R)-Piperidine-2-carboxylic acidHMDB
(R)-()-2-Piperidinecarboxylic acidHMDB
(R)-(+)-Pipecolic acidHMDB
(R)-2-Piperidinecarboxylic acidHMDB
(R)-Pipecolinic acidHMDB
D-(+)- Pipecolic acidHMDB
D-(+)-Pipecolic acidHMDB
D-HomoprolineHMDB
D-Pipecolinic acidHMDB
D-Piperidine-2-carboxylic acidHMDB
Chemical FormulaC6H11NO2
Average Molecular Weight129.157
Monoisotopic Molecular Weight129.078978601
IUPAC Name(2R)-piperidine-2-carboxylic acid
Traditional Name(+)-pipecolic acid
CAS Registry Number1723-00-8
SMILES
OC(=O)[C@H]1CCCCN1
InChI Identifier
InChI=1S/C6H11NO2/c8-6(9)5-3-1-2-4-7-5/h5,7H,1-4H2,(H,8,9)/t5-/m1/s1
InChI KeyHXEACLLIILLPRG-RXMQYKEDSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom.
KingdomChemical entities
Super ClassOrganic compounds
ClassOrganic acids and derivatives
Sub ClassCarboxylic acids and derivatives
Direct ParentD-alpha-amino acids
Alternative Parents
Substituents
  • D-alpha-amino acid
  • Piperidinecarboxylic acid
  • Piperidine
  • Amino acid
  • Carboxylic acid
  • Secondary aliphatic amine
  • Monocarboxylic acid or derivatives
  • Secondary amine
  • Organoheterocyclic compound
  • Azacycle
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Carbonyl group
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect

Health effect:

  Health condition:

    Hepatobiliary disorders:

Disposition

Biological Location:

  Biofluid and excreta:

Source:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point266 - 268 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility158 g/LALOGPS
logP-2.2ALOGPS
logP-2.1ChemAxon
logS0.09ALOGPS
pKa (Strongest Acidic)2.06ChemAxon
pKa (Strongest Basic)10.39ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area49.33 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity32.67 m³·mol⁻¹ChemAxon
Polarizability13.47 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-001i-9100000000-335cf7f41fca5cbc84cfView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-001i-9100000000-4611bf819d3b9d4fd062View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-3900000000-bf71d20a7c8e71d335e5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-9400000000-fa70645b026293d659deView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-053u-9000000000-f849cc3c4b11bc7d4de7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-2900000000-bf800b5cd197887a11d5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-003r-7900000000-8a0e9f51df4006740863View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-001i-9000000000-effc196b5c15971f985aView in MoNA
Biological Properties
Cellular LocationsNot Available
Biofluid Locations
  • Blood
Tissue LocationNot Available
PathwaysNot Available
NameSMPDB/PathwhizKEGG
No entries found
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.11 +/- 0.10 uMAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.16 +/- 0.14 uMAdult (>18 years old)BothUremia details
BloodDetected and Quantified1.58 +/- 0.50 uMAdult (>18 years old)Both
Hepatic Encephalopathy
details
Associated Disorders and Diseases
Disease References
Hepatic encephalopathy
  1. Fujita T, Amuro Y, Hada T, Higashino K: Plasma levels of pipecolic acid, both L- and D-enantiomers, in patients with chronic liver diseases, especially hepatic encephalopathy. Clin Chim Acta. 1999 Sep;287(1-2):99-109. [PubMed:10509899 ]
Uremia
  1. Fujita T, Amuro Y, Hada T, Higashino K: Plasma levels of pipecolic acid, both L- and D-enantiomers, in patients with chronic liver diseases, especially hepatic encephalopathy. Clin Chim Acta. 1999 Sep;287(1-2):99-109. [PubMed:10509899 ]
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB023791
KNApSAcK IDNot Available
Chemspider ID643442
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound736316
PDB IDCPI
ChEBI ID41582
References
Synthesis ReferenceFadel, Antoine; Lahrache, Nabil. An efficient synthesis of enantiomerically pure (R)-pipecolic acid, (S)-proline, and their N-alkylated derivatives. Journal of Organic Chemistry (2007), 72(5), 1780-1784.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Lam S: Stereoselective analysis of D and L dansyl amino acids as the mixed chelate copper(II) complexes by HPLC. J Chromatogr Sci. 1984 Sep;22(9):416-23. [PubMed:6490790 ]
  2. Lam S, Azumaya H, Karmen A: High-performance liquid chromatography of amino acids in urine and cerebrospinal fluid. J Chromatogr. 1984 Oct 19;302:21-9. [PubMed:6501504 ]
  3. Rashed MS, Al-Ahaidib LY, Aboul-Enein HY, Al-Amoudi M, Jacob M: Determination of L-pipecolic acid in plasma using chiral liquid chromatography-electrospray tandem mass spectrometry. Clin Chem. 2001 Dec;47(12):2124-30. [PubMed:11719476 ]
  4. Armstrong DW, Gasper M, Lee SH, Zukowski J, Ercal N: D-amino acid levels in human physiological fluids. Chirality. 1993;5(5):375-8. [PubMed:8398594 ]