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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2007-04-12 18:42:28 UTC
Update Date2021-10-13 04:47:45 UTC
HMDB IDHMDB0005960
Secondary Accession Numbers
  • HMDB0062767
  • HMDB05960
  • HMDB62767
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
Data?1582752369
Synonyms
ValueSource
(R)-Pipecolic acidChEBI
(R)-Piperidine-2-carboxylic acidChEBI
6-CARBOXYPIPERIDINEChEBI
(R)-PipecolateGenerator
(R)-Piperidine-2-carboxylateGenerator
D-PipecolateGenerator
(+)-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
Description Belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
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

Adverse health effect

Disposition

Biological location

Source

Route of exposure

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point266 - 268 °CNot Available
Boiling Point265.80 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility74060 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Spectral PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility158 g/LALOGPS
logP10(-2.2) g/LALOGPS
logP10(-2.1) g/LChemAxon
logS10(0.09) g/LALOGPS
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Spectral Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+128.24531661259
DarkChem[M-H]-122.87731661259

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
D-Pipecolic acid,1TMS,#1C[Si](C)(C)OC(=O)[C@H]1CCCCN11261.2Semi standard non polarhttps://arxiv.org/abs/1905.12712
D-Pipecolic acid,1TMS,#2C[Si](C)(C)N1CCCC[C@@H]1C(=O)O1355.4Semi standard non polarhttps://arxiv.org/abs/1905.12712
D-Pipecolic acid,1TBDMS,#1CC(C)(C)[Si](C)(C)OC(=O)[C@H]1CCCCN11500.1Semi standard non polarhttps://arxiv.org/abs/1905.12712
D-Pipecolic acid,1TBDMS,#2CC(C)(C)[Si](C)(C)N1CCCC[C@@H]1C(=O)O1575.4Semi standard non polarhttps://arxiv.org/abs/1905.12712
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - D-Pipecolic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-001i-9100000000-335cf7f41fca5cbc84cf2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Pipecolic acid GC-MS (1 TMS) - 70eV, Positivesplash10-001i-9100000000-4611bf819d3b9d4fd0622017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Pipecolic 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 - D-Pipecolic acid 10V, Positive-QTOFsplash10-001i-3900000000-bf71d20a7c8e71d335e52017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 20V, Positive-QTOFsplash10-001i-9400000000-fa70645b026293d659de2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 40V, Positive-QTOFsplash10-053u-9000000000-f849cc3c4b11bc7d4de72017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 10V, Negative-QTOFsplash10-004i-2900000000-bf800b5cd197887a11d52017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 20V, Negative-QTOFsplash10-003r-7900000000-8a0e9f51df40067408632017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 40V, Negative-QTOFsplash10-001i-9000000000-effc196b5c15971f985a2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 10V, Positive-QTOFsplash10-001i-9300000000-cb8df30f7267d610fd8d2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 20V, Positive-QTOFsplash10-001i-9000000000-72c8691eb15dce6e0abb2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 40V, Positive-QTOFsplash10-053r-9000000000-c7623c5058ad6c879ec32021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 10V, Negative-QTOFsplash10-004i-0900000000-b487cd2a72f17977a8cd2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 20V, Negative-QTOFsplash10-01t9-1900000000-83b59287dc6d3e7263262021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 40V, Negative-QTOFsplash10-0036-9200000000-3ca813e7348e686ed9222021-09-24Wishart 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
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.11 +/- 0.10 uMAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
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
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 ]
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 ]
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023791
KNApSAcK IDNot Available
Chemspider ID643442
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPipecolic acid
METLIN IDNot Available
PubChem Compound736316
PDB IDNot Available
ChEBI ID41582
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00000476
Good Scents IDrw1234121
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 ]