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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2016-02-11 01:03:16 UTC
HMDB IDHMDB00716
Secondary Accession NumbersNone
Metabolite Identification
Common NameL-Pipecolic acid
DescriptionL-Pipecolic acid is a normal human metabolite present in human blood, where is present as the primary enantiomer of pipecolic acid. L-Pipecolic acid is a cyclic imino acid produced during the degradation of lysine, accumulates in body fluids of infants with generalized genetic peroxisomal disorders, including Zellweger syndrome (OMIM 214100 ), neonatal adrenoleukodystrophy (OMIM 202370 ), and infantile Refsum disease (OMIM 266510 ). L-Pipecolic acid levels are also elevated in patients with chronic liver diseases. L-Pipecolic acid is the substrate of delta1-piperideine-2-carboxylate reductase [EC 1.5.1.21] in the pathway of lysine degradation. (PMID: 2717271 , 8305590 , 1050990 ).
Structure
Thumb
Synonyms
ValueSource
(S)-(-)-Pipecolic acidChEBI
(S)-Pipecolic acidChEBI
(S)-Piperidine-2-carboxylic acidChEBI
2-Piperidinecarboxylic acidChEBI
L-(-)-Pipecolic acidChEBI
Pipecolic acidChEBI
Pipecolinic acidChEBI
(S)-(-)-PipecolateGenerator
L-PipecolateGenerator
(S)-PipecolateGenerator
(S)-Piperidine-2-carboxylateGenerator
2-PiperidinecarboxylateGenerator
L-(-)-PipecolateGenerator
PipecolateGenerator
PipecolinateGenerator
(-)-PipecolateHMDB
(-)-Pipecolic acidHMDB
(S)-(-)-2-PiperidinecarboxylateHMDB
(S)-(-)-2-Piperidinecarboxylic acidHMDB
(S)-2-PiperidinecarboxylateHMDB
(S)-2-Piperidinecarboxylic acidHMDB
(S)-PipecolinateHMDB
(S)-Pipecolinic acidHMDB
L-HomoprolineHMDB
L-PipecolinateHMDB
L-Pipecolinic acidHMDB
L-Piperidine-2-carboxylateHMDB
L-Piperidine-2-carboxylic acidHMDB
Chemical FormulaC6H11NO2
Average Molecular Weight129.157
Monoisotopic Molecular Weight129.078978601
IUPAC Name(2S)-piperidine-2-carboxylic acid
Traditional NameL-pipecolic acid
CAS Registry Number3105-95-1
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-/m0/s1
InChI KeyInChIKey=HXEACLLIILLPRG-YFKPBYRVSA-N
Chemical Taxonomy
DescriptionThis compound 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
  • Azacycle
  • Organoheterocyclic compound
  • Secondary amine
  • Monocarboxylic acid or derivatives
  • Secondary aliphatic amine
  • Carboxylic acid
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Amine
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
Biofunction
  • Protein synthesis, amino acid biosynthesis
ApplicationNot Available
Cellular locations
  • Peroxisome
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point272 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility158.0 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count1ChemAxon
Refractivity32.67 m3·mol-1ChemAxon
Polarizability13.49 Å3ChemAxon
Number of Rings1ChemAxon
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)splash10-0a4i-0900000000-c7875e682dfb275cdf1eView in MoNA
GC-MSGC-MS Spectrum - GC-MS (1 TMS)splash10-001i-9100000000-07741b1b7d650447197eView in MoNA
GC-MSGC-MS Spectrum - GC-MS (2 TMS)splash10-0a4i-1900000000-1b1313072749567d8a9eView in MoNA
GC-MSGC-MS Spectrum - GC-MS (1 MEOX; 2 TMS)splash10-0pb9-3960000000-8e89c177d71b5faabdb2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, N/A (Annotated)splash10-001i-8900000000-b67eb6eabd8fb1b2824aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, N/A (Annotated)splash10-001i-9000000000-b01a5574139ce1222c4dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, N/A (Annotated)splash10-0a4i-9000000000-d80733b289711920626bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-004i-0900000000-6d82525e15d98dd794dbView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-004i-0900000000-abb8b4f2daaa91bfa758View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-004i-1900000000-b668d1df137fa1685b6dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0002-9000000000-5ec763c9c55715bd01dfView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0002-9000000000-5a62167bd787768808f7View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-001i-0900000000-edd41fa2c224ec5f5a1eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-001i-9100000000-7ed3d7197cd0f23403b6View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-001i-9000000000-e5b2220b7410a3429b95View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-001i-9000000000-baf8dab4263881ac49eaView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-0a59-9000000000-d1dc7829582bfd61d47bView in MoNA
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
Biological Properties
Cellular Locations
  • Peroxisome
Biofluid Locations
  • Blood
  • Feces
Tissue Location
  • Liver
Pathways
NameSMPDB LinkKEGG Link
2-aminoadipic 2-oxoadipic aciduriaSMP00719Not Available
Glutaric Aciduria Type ISMP00186Not Available
Hyperlysinemia I, FamilialSMP00527Not Available
Hyperlysinemia II or SaccharopinuriaSMP00528Not Available
Lysine DegradationSMP00037map00310
Pyridoxine dependency with seizuresSMP00571Not Available
Saccharopinuria/Hyperlysinemia IISMP00239Not Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified10.0 (0.0-20.0) uMChildren (1-13 years old)BothNormal
    • Geigy Scientific ...
details
FecesDetected but not QuantifiedNot ApplicableNot SpecifiedNot Specified
Normal
details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified9.7 +/- 3.1 uMAdult (>18 years old)BothZellweger syndrome details
BloodDetected and Quantified65.0 +/- 63.0 uMNewborn (0-30 days old)BothAdrenoleukodystrophy (ALD) details
Associated Disorders and Diseases
Disease References
Adrenoleukodystrophy
  1. Watkins PA, Chen WW, Harris CJ, Hoefler G, Hoefler S, Blake DC Jr, Balfe A, Kelley RI, Moser AB, Beard ME, et al.: Peroxisomal bifunctional enzyme deficiency. J Clin Invest. 1989 Mar;83(3):771-7. [2921319 ]
Peroxisomal biogenesis defect
  1. Watkins PA, Chen WW, Harris CJ, Hoefler G, Hoefler S, Blake DC Jr, Balfe A, Kelley RI, Moser AB, Beard ME, et al.: Peroxisomal bifunctional enzyme deficiency. J Clin Invest. 1989 Mar;83(3):771-7. [2921319 ]
Associated OMIM IDs
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB000546
KNApSAcK IDNot Available
Chemspider ID388365
KEGG Compound IDC00408
BioCyc IDL-PIPECOLATE
BiGG ID34890
Wikipedia LinkNot Available
NuGOwiki LinkHMDB00716
Metagene LinkHMDB00716
METLIN ID5684
PubChem Compound439227
PDB IDYCP
ChEBI ID30913
References
Synthesis ReferenceKisfaludy, Lajos; Korenczki, Ferenc; Katho, Agnes. Works, Gedeon Richter Ltd., Budapest, Hung. One-step synthesis of L-piperidine-2-carboxylic acid. Synthesis (1982), (2), 163.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Mihalik SJ, Moser HW, Watkins PA, Danks DM, Poulos A, Rhead WJ: Peroxisomal L-pipecolic acid oxidation is deficient in liver from Zellweger syndrome patients. Pediatr Res. 1989 May;25(5):548-52. [2717271 ]
  2. Baumgartner MR, Jansen GA, Verhoeven NM, Mooyer PA, Jakobs C, Roels F, Espeel M, Fourmaintraux A, Bellet H, Wanders RJ, Saudubray JM: Atypical refsum disease with pipecolic acidemia and abnormal catalase distribution. Ann Neurol. 2000 Jan;47(1):109-13. [10632109 ]
  3. 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. [6490790 ]
  4. Armstrong DW, Zukowski J, Ercal N, Gasper M: Stereochemistry of pipecolic acid found in the urine and plasma of subjects with peroxisomal deficiencies. J Pharm Biomed Anal. 1993 Oct;11(10):881-6. [8305590 ]
  5. Langeland R: [Construction of facilities in the health sector]. Sykepleien. 1976 Sep 5;63(15):782-4, 793. [1050990 ]

Enzymes

General function:
Involved in oxidoreductase activity
Specific function:
Metabolizes sarcosine, L-pipecolic acid and L-proline.
Gene Name:
PIPOX
Uniprot ID:
Q9P0Z9
Molecular weight:
44065.515
Reactions
L-Pipecolic acid + Oxygen → (S)-2,3,4,5-tetrahydropyridine-2-carboxylate + Hydrogen peroxidedetails