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Record Information
Created at2005-11-16 15:48:42 UTC
Updated at2021-10-07 20:42:25 UTC
NP-MRD IDNP0001452
Secondary Accession NumbersNone
Natural Product Identification
Common NamePipecolic acid
DescriptionPipecolic acid is a metabolite of lysine found in human physiological fluids such as urine, plasma and CSF. However, it is uncertain if pipecolic acid originates directly from food intake or from mammalian or intestinal bacterial enzyme metabolism. Recent studies suggest that plasma pipecolic acid, particularly the D-isomer, originates mainly from the catabolism of dietary lysine by intestinal bacteria rather than by direct food intake. In classic Zellweger syndrome (a cerebro-hepato-renal genetic disorder, OMIM 214100 ) pipecolic acid accumulate in the plasma of the patients. It is known that plasma pipecolic acid levels are also elevated in patients with chronic liver diseases. Pipecolic acid is moderately elevated in patients with pyridoxine-dependent seizures and might therefore be a possible biochemical marker for selecting candidates for pyridoxine therapy (Plecko et al 2000). Pipecolic acid was also elevated in CSF in these vitamin B6-responsive patients (PMID 12705501 ). Pipecolic acid is found to be associated with adrenoleukodystrophy, infantile Refsum disease, and peroxisomal biogenesis defect, which are also inborn errors of metabolism. Pipecolic acid is a biomarker for the consumption of dried and cooked beans.
2-Piperidinecarboxylic acidChEBI
Pipecolinic acidChEBI
()-Piperidine-2-carboxylic acidHMDB
(+/-)-2-piperidinecarboxylic acidHMDB
(+/-)-pipecolic acidHMDB
(+/-)-pipecolinic acidHMDB
(.+/-.)-2-piperidinecarboxylic acidHMDB
(RS)-2-Piperidinecarboxylic acidHMDB
.alpha.-pipecolinic acidHMDB
2-Pipecolinic acidHMDB
2-Piperidinylcarboxylic acidHMDB
a-Pipecolinic acidHMDB
Acide pipecoliqueHMDB
Acide piperidine-carboxylique-2HMDB
alpha-Pipecolinic acidHMDB
DL-2-Piperidinecarboxylic acidHMDB
DL-Pipecolic acidHMDB
DL-Pipecolinic acidHMDB
Hexahydro-2-picolinic acidHMDB
Hexahydropicolinic acidHMDB
Pipecolic acid free baseHMDB
Piperidine-2-carboxylic acidHMDB
Piperolinic acidHMDB
L-Pipecolic acidHMDB
Pipecolic acid, (R)-isomerHMDB
Pipecolic acid, ion (1-)HMDB
Pipecolic acid, monopotassium saltHMDB
Pipecolic acid hydrochloride, (+-)-isomerHMDB
Pipecolic acid, (S)-isomerHMDB
Pipecolic acid, 14C-labeled CPD, (+,-)-isomerHMDB
Homopipecolic acidHMDB
Pipecolic acid, (+,-)-isomerHMDB
Pipecolic acid, ion(1-), (+,-)-isomerHMDB
Pipecolic acid, ion(1-), (S)-isomerHMDB
Pipecolic acidMeSH
Chemical FormulaC6H11NO2
Average Mass129.1570 Da
Monoisotopic Mass129.07898 Da
IUPAC Namepiperidine-2-carboxylic acid
Traditional Name(+,-)-pipecolic acid
CAS Registry Number535-75-1
InChI Identifier
Spectrum TypeDescriptionDepositor IDDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart Lab2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart Lab2021-06-20View Spectrum
Species of Origin
Species NameSourceReference
Castanea sativaKNApSAcK Database
Daucus carotaFooDB
Daucus carota ssp. sativusFooDB
Lemna gibbaKNApSAcK Database
Lemna paucicostataKNApSAcK Database
Lupinus albusFooDB
Malus pumilaFooDB
Momordica charantiaFooDB
Musa x paradisiacaFooDB
Phaseolus vulgarisKNApSAcK Database
Phoenix dactyliferaFooDB
Pisum sativumFooDB
Prunus cerasusFooDB
Solanum lycopersicum var. lycopersicumFooDB
Solanum melongenaFooDB
Tamarindus indicaFooDB
Vicia fabaFooDB
Vigna angularisFooDB
Zingiber officinaleFooDB
Species Where Detected
Species NameSourceReference
Alternaria oxytropis Raft RiverKNApSAcK Database
Arthroderma otae CBS113480KNApSAcK Database
Phoma medicaginisKNApSAcK Database
Trichophyton equinum CBS127.97KNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids
Alternative Parents
  • Alpha-amino acid
  • Piperidinecarboxylic acid
  • Piperidine
  • Amino acid
  • Azacycle
  • Organoheterocyclic compound
  • Secondary amine
  • Monocarboxylic acid or derivatives
  • Secondary aliphatic amine
  • Carboxylic acid
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Amine
  • Organic nitrogen compound
  • Organic oxide
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
Experimental Properties
Melting Point264 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility314 mg/mLNot Available
LogP-2.31Tsai, R. S., Testa, B., El Tayar, N., & Carrupt, P. A. (1991). Structure-lipophilicity relationships of zwitterionic amino acids. Journal of the Chemical Society, Perkin Transactions 2, (11), 1797-1802.
Predicted Properties
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
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB000545
KNApSAcK IDC00001387
Chemspider ID826
KEGG Compound IDC00408
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPipecolic_acid
PubChem Compound849
PDB IDNot Available
ChEBI ID17964
Good Scents IDrw1586071
General References
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
  2. Kawasaki H, Hori T, Nakajima M, Takeshita K: Plasma levels of pipecolic acid in patients with chronic liver disease. Hepatology. 1988 Mar-Apr;8(2):286-9. [PubMed:3356409 ]
  3. Chang YF: Lysine metabolism in the human and the monkey: demonstration of pipecolic acid formation in the brain and other organs. Neurochem Res. 1982 May;7(5):577-88. [PubMed:6811962 ]
  4. van den Berg GA, Breukelman H, Elzinga H, Trijbels JM, Monnens LA, Muskiet FA: Determination of pipecolic acid in urine and plasma by isotope dilution mass fragmentography. Clin Chim Acta. 1986 Sep 30;159(3):229-37. [PubMed:3769211 ]
  5. Medana IM, Hien TT, Day NP, Phu NH, Mai NT, Chu'ong LV, Chau TT, Taylor A, Salahifar H, Stocker R, Smythe G, Turner GD, Farrar J, White NJ, Hunt NH: The clinical significance of cerebrospinal fluid levels of kynurenine pathway metabolites and lactate in severe malaria. J Infect Dis. 2002 Mar 1;185(5):650-6. Epub 2002 Feb 14. [PubMed:11865422 ]
  6. Danks DM, Tippett P, Adams C, Campbell P: Cerebro-hepato-renal syndrome of Zellweger. A report of eight cases with comments upon the incidence, the liver lesion, and a fault in pipecolic acid metabolism. J Pediatr. 1975 Mar;86(3):382-7. [PubMed:1113225 ]
  7. Plecko B, Stockler-Ipsiroglu S, Paschke E, Erwa W, Struys EA, Jakobs C: Pipecolic acid elevation in plasma and cerebrospinal fluid of two patients with pyridoxine-dependent epilepsy. Ann Neurol. 2000 Jul;48(1):121-5. [PubMed:10894227 ]
  8. Burton BK, Reed SP, Remy WT: Hyperpipecolic acidemia: clinical and biochemical observations in two male siblings. J Pediatr. 1981 Nov;99(5):729-34. [PubMed:7299546 ]
  9. Smythe GA, Poljak A, Bustamante S, Braga O, Maxwell A, Grant R, Sachdev P: ECNI GC-MS analysis of picolinic and quinolinic acids and their amides in human plasma, CSF, and brain tissue. Adv Exp Med Biol. 2003;527:705-12. [PubMed:15206793 ]
  10. Trijbels JM, Monnens LA, Melis G, van den Broekvan Essen M, Bruckwilder M: Localization of pipecolic acid metabolism in rat liver peroxisomes: probable explanation for hyperpipecolataemia in Zellweger syndrome. J Inherit Metab Dis. 1987;10(2):128-34. [PubMed:3116331 ]
  11. Thomas GH, Haslam RH, Batshaw ML, Capute AJ, Neidengard L, Ransom JL: Hyperpipecolic acidemia associated with hepatomegaly, mental retardation, optic nerve dysplasia and progressive neurological disease. Clin Genet. 1975 Nov;8(5):376-82. [PubMed:1204235 ]
  12. Medana IM, Day NP, Salahifar-Sabet H, Stocker R, Smythe G, Bwanaisa L, Njobvu A, Kayira K, Turner GD, Taylor TE, Hunt NH: Metabolites of the kynurenine pathway of tryptophan metabolism in the cerebrospinal fluid of Malawian children with malaria. J Infect Dis. 2003 Sep 15;188(6):844-9. Epub 2003 Sep 9. [PubMed:12964115 ]
  13. Lee HF, Mak SC, Wu FW, Chi CS, Huang SC: Zellweger syndrome: report of one case. Acta Paediatr Taiwan. 2001 Jan-Feb;42(1):53-6. [PubMed:11270189 ]
  14. Kok RM, Kaster L, de Jong AP, Poll-The B, Saudubray JM, Jakobs C: Stable isotope dilution analysis of pipecolic acid in cerebrospinal fluid, plasma, urine and amniotic fluid using electron capture negative ion mass fragmentography. Clin Chim Acta. 1987 Sep 30;168(2):143-52. [PubMed:3315316 ]
  15. Baas JC, van de Laar R, Dorland L, Duran M, Berger R, Poll-The BT, de Koning TJ: Plasma pipecolic acid is frequently elevated in non-peroxisomal disease. J Inherit Metab Dis. 2002 Dec;25(8):699-701. [PubMed:12705501 ]
  16. Dancis J, Hutzler J: Comparative rates of metabolism of pipecolic acid in several animal species. Comp Biochem Physiol B. 1982;73(4):1011-2. [PubMed:6817963 ]
  17. Fujita T, Hada T, Higashino K: Origin of D- and L-pipecolic acid in human physiological fluids: a study of the catabolic mechanism to pipecolic acid using the lysine loading test. Clin Chim Acta. 1999 Sep;287(1-2):145-56. [PubMed:10509903 ]