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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2021-09-14 15:45:28 UTC
HMDB IDHMDB0000716
Secondary Accession Numbers
  • HMDB00716
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 (contains both imino (>C=NH) and carboxyl (-C(=O)-OH) functional groups) 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
Data?1582752151
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
(S)-PipecolateGenerator
(S)-Piperidine-2-carboxylateGenerator
2-PiperidinecarboxylateGenerator
L-(-)-PipecolateGenerator
PipecolateGenerator
PipecolinateGenerator
L-PipecolateGenerator
(-)-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
Pipecolic acid, (+,-)-isomerHMDB
Pipecolic acid, 14C-labeled CPD, (+,-)-isomerHMDB
Homopipecolic acidHMDB
Pipecolic acid, ion(1-), (+,-)-isomerHMDB
Pipecolic acid, ion(1-), (S)-isomerHMDB
Pipecolic acid hydrochloride, (+-)-isomerHMDB
Pipecolic acid, (S)-isomerHMDB
Pipecolic acid, (R)-isomerHMDB
Pipecolic acid, ion (1-)HMDB
Pipecolic acid, monopotassium saltHMDB
(2S)-2-Piperidinecarboxylic acidPhytoBank
(-)-Pipecolinic acidPhytoBank
(2S)-Piperidine-2-carboxylic acidPhytoBank
L-Pipecolic acidPhytoBank
(RS)-2-Piperidinecarboxylic acidPhytoBank
(±)-2-Piperidinecarboxylic acidPhytoBank
(±)-Pipecolic acidPhytoBank
(±)-Pipecolinic acidPhytoBank
2-CarboxypiperidinePhytoBank
2-Pipecolinic acidPhytoBank
2-Piperidinylcarboxylic acidPhytoBank
DL-2-Piperidinecarboxylic acidPhytoBank
DL-Pipecolic acidPhytoBank
DL-Pipecolinic acidPhytoBank
DihydrobaikianePhytoBank
Hexahydro-2-picolinic acidPhytoBank
HomoprolinePhytoBank
Piperidine-6-carboxylic acidPhytoBank
Piperolinic acidPhytoBank
alpha-Pipecolinic acidPhytoBank
α-Pipecolinic acidPhytoBank
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 KeyHXEACLLIILLPRG-YFKPBYRVSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentL-alpha-amino acids
Alternative Parents
Substituents
  • L-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:

Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point272 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Molecular 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
Polarizability13.49 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Spectral Properties

Collision Cross Sections

NameAdductTypeData SourceValueReference
DeepCCS[M-H]-ExperimentalBaker133.81530932474
DeepCCS[M-H]-ExperimentalMetCCS_train_neg126.71330932474
DeepCCS[M+H]+ExperimentalBaker130.93330932474
DeepCCS[M+H]+ExperimentalMetCCS_train_pos127.40230932474
AllCCS[M-H]-ExperimentalNot Available128.6http://allccs.zhulab.cn/database/detail?ID=AllCCS00000028
AllCCS[M+H]+ExperimentalNot Available128.4http://allccs.zhulab.cn/database/detail?ID=AllCCS00000028
DarkChem[M+H]+PredictedNot Available127.9531661259
DarkChem[M-H]-PredictedNot Available121.60231661259
AllCCS[M+H]+PredictedNot Available127.91432859911
AllCCS[M-H]-PredictedNot Available125.3132859911

Retention Indices

Underivatized

Not Available

Derivatized

DerivativeValueReference
L-Pipecolic acid,1TMS,#11261.2277https://arxiv.org/abs/1905.12712
L-Pipecolic acid,1TMS,#21355.4142https://arxiv.org/abs/1905.12712
L-Pipecolic acid,1TBDMS,#11500.0786https://arxiv.org/abs/1905.12712
L-Pipecolic acid,1TBDMS,#21575.3638https://arxiv.org/abs/1905.12712
Spectra

GC-MS

Spectrum TypeDescriptionSplash KeyDeposition DateView
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-0a4i-0900000000-c7875e682dfb275cdf1e2014-06-16View Spectrum
GC-MSGC-MS Spectrum - GC-MS (1 TMS)splash10-001i-9100000000-07741b1b7d650447197e2014-06-16View Spectrum
GC-MSGC-MS Spectrum - GC-MS (2 TMS)splash10-0a4i-1900000000-1b1313072749567d8a9e2014-06-16View Spectrum
GC-MSGC-MS Spectrum - GC-MS (1 MEOX; 2 TMS)splash10-0pb9-3960000000-8e89c177d71b5faabdb22014-06-16View Spectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0a4i-0900000000-c7875e682dfb275cdf1e2017-09-12View Spectrum
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0a4i-1900000000-1b1313072749567d8a9e2017-09-12View Spectrum
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0pb9-3960000000-8e89c177d71b5faabdb22017-09-12View Spectrum
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-001i-9100000000-07741b1b7d650447197e2017-09-12View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-001i-9100000000-335cf7f41fca5cbc84cf2017-09-01View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-05fu-9700000000-8003521353d4d37af49f2017-10-06View Spectrum
MSMass Spectrum (Electron Ionization)splash10-001i-9100000000-335cf7f41fca5cbc84cf2021-09-05View Spectrum
MSMass Spectrum (Electron Ionization)splash10-0a4i-8900000000-5b42adf83e422cffefb62021-09-18View Spectrum
MSMass Spectrum (Electron Ionization)splash10-0a4i-9800000000-24fa3ff739ff064312ab2021-09-18View Spectrum

LC-MS/MS

Spectrum TypeDescriptionSplash KeyDeposition DateView
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, N/A (Annotated)splash10-001i-8900000000-b67eb6eabd8fb1b2824a2012-07-24View Spectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, N/A (Annotated)splash10-001i-9000000000-b01a5574139ce1222c4d2012-07-24View Spectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, N/A (Annotated)splash10-0a4i-9000000000-d80733b289711920626b2012-07-24View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-004i-0900000000-6d82525e15d98dd794db2012-08-31View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-004i-0900000000-abb8b4f2daaa91bfa7582012-08-31View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-004i-1900000000-b668d1df137fa1685b6d2012-08-31View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0002-9000000000-5ec763c9c55715bd01df2012-08-31View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0002-9000000000-5a62167bd787768808f72012-08-31View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-004i-0900000000-6d82525e15d98dd794db2017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-004i-0900000000-abb8b4f2daaa91bfa7582017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-004i-1900000000-b668d1df137fa1685b6d2017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0002-9000000000-5ec763c9c55715bd01df2017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0002-9000000000-5a62167bd787768808f72017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-001i-0900000000-edd41fa2c224ec5f5a1e2012-08-31View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-001i-9100000000-7ed3d7197cd0f23403b62012-08-31View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-001i-9000000000-e5b2220b7410a3429b952012-08-31View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-001i-9000000000-baf8dab4263881ac49ea2012-08-31View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-0a59-9000000000-d1dc7829582bfd61d47b2012-08-31View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-001i-0900000000-edd41fa2c224ec5f5a1e2017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-001i-9100000000-a4a80ec7473a698297952017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-001i-9000000000-e5b2220b7410a3429b952017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-001i-9000000000-e5a8f35e91abe8d99ac52017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0a59-9000000000-d1dc7829582bfd61d47b2017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT , positivesplash10-001i-9000000000-4c79a7eb98fbfc7dc32e2017-09-14View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-2900000000-bf800b5cd197887a11d52017-09-01View Spectrum

NMR

Spectrum TypeDescriptionDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)2012-12-04View Spectrum
2D NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, H2O, predicted)2012-12-05View Spectrum
Biological Properties
Cellular Locations
  • Peroxisome
Biospecimen Locations
  • Blood
  • Feces
Tissue Locations
  • Liver
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified10.0 (0.0-20.0) uMChildren (1-13 years old)BothNormal
    • Geigy Scientific ...
details
BloodDetected and Quantified2.46 +/- 1.26 uMAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
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
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. [PubMed:2921319 ]
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. [PubMed:2921319 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB000546
KNApSAcK IDC00001387
Chemspider ID388365
KEGG Compound IDC00408
BioCyc IDL-PIPECOLATE
BiGG ID34890
Wikipedia LinkPipecolic acid
METLIN ID5684
PubChem Compound439227
PDB IDNot Available
ChEBI ID30913
Food Biomarker OntologyNot Available
VMH IDLPIPECOL
MarkerDB IDMDB00000233
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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed:8305590 ]
  5. Langeland R: [Construction of facilities in the health sector]. Sykepleien. 1976 Sep 5;63(15):782-4, 793. [PubMed: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 → 2,3,4,5-Tetrahydro-2-pyridinecarboxylic acid + Hydrogen peroxidedetails