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Human Metabolome Database Version 2.5

 

Showing metabocard for L-Pipecolic acid (HMDB00716)

Legend: metabolite field enzyme field

Version 2.5
Creation Date 2005-11-16 15:48:42
Update Date 2010-05-10 16:23:16
Accession Number HMDB00716
Secondary Accession Numbers Not Available
Common Name L-Pipecolic acid
Description L-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)
Synonyms
  1. (-)-Pipecolate
  2. (-)-Pipecolic acid
  3. (S)-(-)-2-Piperidinecarboxylate
  4. (S)-(-)-2-Piperidinecarboxylic acid
  5. (S)-(-)-Pipecolate
  6. (S)-(-)-Pipecolic acid
  7. (S)-2-Piperidinecarboxylate
  8. (S)-2-Piperidinecarboxylic acid
  9. (S)-Pipecolate
  10. (S)-Pipecolic acid
  11. (S)-Pipecolinate
  12. (S)-Pipecolinic acid
  13. (S)-Piperidine-2-carboxylate
  14. (S)-Piperidine-2-carboxylic acid
  15. L-(-)-Pipecolate
  16. L-(-)-Pipecolic acid
  17. L-Homoproline
  18. L-Pipecolate
  19. L-Pipecolic acid
  20. L-Pipecolinate
  21. L-Pipecolinic acid
  22. L-Piperidine-2-carboxylate
  23. L-Piperidine-2-carboxylic acid
Chemical IUPAC Name (2S)-piperidine-2-carboxylic acid
Chemical Formula C6H11NO2
Chemical Structure Structure
Chemical Taxonomy
Kingdom
  • Organic
Super Class
  • Amino acids and Amino Acid conjugates
Class
  • Amino Acids
Sub Class
  • NA
Family
  • Mammalian Metabolite
Species
  • secondary amine
  • secondary aliphatic amine (dialkylamine)
  • carboxylic acid
  • heterocyclic compound
  • alpha-aminoacid
Biofunction
  • Protein synthesis, amino acid biosynthesis
Application
—
Source
  • Endogenous
Average Molecular Weight 129.157
Monoisotopic Molecular Weight 129.078979
Isomeric SMILES OC(=O)[C@@H]1CCCCN1
Canonical SMILES OC(=O)C1CCCCN1
KEGG Compound ID C00408 Link Image
BioCyc ID L-PIPECOLATE Link Image
BiGG ID 34890 Link Image
Wikipedia Link Not Available
NuGOwiki Link HMDB00716 Link Image
Metagene Link HMDB00716 Link Image
METLIN ID 5684 Link Image
PubChem Compound 439227 Link Image
PubChem Substance 26744347 Link Image
ChEBI ID 30913 Link Image
CAS Registry Number 3105-95-1
InChI Identifier InChI=1/C6H11NO2/c8-6(9)5-3-1-2-4-7-5/h5,7H,1-4H2,(H,8,9)/t5-/m0/s1
Synthesis Reference Kisfaludy, Lajos; Korenczki, Ferenc; Katho, Agnes. Works, Gedeon Richter Ltd., Budapest, Hung. One-step synthesis of L-piperidine-2-carboxylic acid. Synthesis (1982), (2), 163.
Melting Point (Experimental) 272 oC
Experimental Water Solubility Not Available Source: PhysProp
Predicted Water Solubility 158.0 mg/mL [Predicted by ALOGPS] Calculated using ALOGPS
Physiological Charge 0
State Solid
Experimental LogP/Hydrophobicity Not Available Source: PhysProp
Predicted LogP/Hydrophobicity -2.17 [Predicted by ALOGPS]; -2 [Predicted by PubChem via XLOGP] Calculated using ALOGPS
Material Safety Data Sheet (MSDS)
MOL File Show
SDF File Show
PDB File Show
2D Structure
3D Structure
Experimental PDB ID Not Available
Experimental 1H NMR Spectrum Download Spectrum
Download FID (Bruker)
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Experimental 13C NMR Spectrum Not Available
Experimental 13C HSQC Spectrum Download Spectrum
Download FID (Bruker)
Show Experimental Conditions Link Image
Predicted 1H NMR Spectrum Show Image
Show Peaklist
Predicted 13C NMR Spectrum Show Image
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Mass Spectrum
Low Energy
Download File
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Medium Energy
Download File
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High Energy
Download File
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Simplified TOCSY Spectrum Not Available
BMRB Spectrum Not Available
Cellular Location
  • peroxisome
Biofluid Location
  • Blood
Tissue Location
Tissue References
Liver —
Concentrations (Normal)
Biofluid Blood
Value 10.0 (0.0-20.0) uM
Age Children:1-13 yrs old
Sex Both
Patient information Normal
Comments Not Available
References
  • Geigy Scientific Tables, 8th Rev edition, pp. 165-177. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp., Basel, Switzerland c1981-1992.
Concentrations (Abnormal)
Biofluid Blood
Value 9.7 +/- 3.1 uM
Age Adult:>18 yrs old
Sex Both
Condition Peroxisomal biogenesis defect
Comments Not Available
References
  • 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 Link Image]
Biofluid Blood
Value 65.0 +/- 63.0 uM
Age Newborn:0-30 days old
Sex Both
Condition Adrenoleukodystrophy
Comments Not Available
References
  • 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 Link Image]
Associated Disorders
Condition References
Adrenoleukodystrophy
  • 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 Link Image]
Peroxisomal biogenesis defect
  • 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 Link Image]
OMIM ID
Pathways
Name SMPDB Link KEGG Link
Lysine Degradation SMP00037 Link Image map00310 Link Image
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 Link Image]
  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 Link Image]
  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 Link Image]
Metabolic Enzymes
  1. Peroxisomal sarcosine oxidase
  2. cDNA FLJ14592 fis, clone NT2RM4002063, highly similar to Peroxisomal sarcosine oxidase (EC 1.5.3.1)
Enzyme 1 [top]
Enzyme 1 ID 5354
Enzyme 1 Name Peroxisomal sarcosine oxidase
Enzyme 1 Synonyms
  1. PSO
  2. L-pipecolate oxidase
  3. L-pipecolic acid oxidase
Enzyme 1 Gene Name PIPOX
Enzyme 1 Protein Sequence >Peroxisomal sarcosine oxidase 
MAAQKDLWDAIVIGAGIQGCFTAYHLAKHRKRILLLEQFFLPHSRGSSHGQSRIIRKAYL
EDFYTRMMHECYQIWAQLEHEAGTQLHRQTGLLLLGMKENQELKTIQANLSRQRVEHQCL
SSEELKQRFPNIRLPRGEVGLLDNSGGVIYAYKALRALQDAIRQLGGIVRDGEKVVEINP
GLLVTVKTTSRSYQAKSLVITAGPWTNQLLRPLGIEMPLQTLRINVCYWREMVPGSYGVS
QAFPCFLWLGLCPHHIYGLPTGEYPGLMKVSYHHGNHADPEERDCPTARTDIGDVQILSS
FVRDHLPDLKPEPAVIESCMYTNTPDEQFILDRHPKYDNIVIGAGFSGHGFKLAPVVGKI
LYELSMKLTPSYDLAPFRISRFPSLGKAHL
Enzyme 1 Number of Residues 390
Enzyme 1 Molecular Weight 44067
Enzyme 1 Theoretical pI 8.54
Enzyme 1 GO Classification
Function
  • catalytic activity
  • oxidoreductase activity
  • oxidoreductase activity, acting on the CH-NH group of donors
  • oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor
  • sarcosine oxidase activity
Process
  • aromatic compound metabolism
  • cellular metabolism
  • electron transport
  • folic acid and derivative metabolism
  • generation of precursor metabolites and energy
  • metabolism
  • physiological process
  • tetrahydrofolate metabolism
Component
—
Enzyme 1 General Function Amino acid transport and metabolism
Enzyme 1 Specific Function Metabolizes sarcosine, L-pipecolic acid and L-proline
Enzyme 1 Pathways
Enzyme 1 Reactions
  • L-pipecolate + O2 = 2,3,4,5-tetrahydropyridine-2-carboxylate + H2O2
Enzyme 1 Pfam Domain Function
Enzyme 1 Signals
  • None
Enzyme 1 Transmembrane Regions
  • 7-26
Enzyme 1 Essentiality Not Available
Enzyme 1 GenBank ID Protein 7157903 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID Q9P0Z9 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name SOX_HUMAN Link Image
Enzyme 1 PDB ID Not Available
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence >1173 bp 
ATGGCGGCTCAGAAAGATCTCTGGGACGCCATTGTGATTGGGGCGGGGATCCAGGGCTGC
TTCACTGCATACCACCTCGCCAAACACAGGAAGAGGATCCTCCTGCTGGAGCAGTTCTTT
CTACCACACTCCCGAGGAAGCTCCCATGGACAAAGCCGGATAATCCGAAAGGCGTACCTG
GAAGACTTTTACACCCGGATGATGCATGAGTGCTATCAGATATGGGCCCAGCTGGAGCAC
GAGGCTGGAACCCAATTGCACAGGCAGACTGGATTACTGCTGCTGGGAATGAAAGAGAAT
CAAGAATTAAAGACAATCCAGGCCAATCTGTCGAGGCAGAGGGTAGAACACCAGTGTCTT
TCATCTGAGGAACTGAAGCAACGTTTCCCAAATATTCGGTTGCCCAGGGGAGAAGTGGGG
CTCTTGGACAATTCCGGAGGAGTTATCTATGCATATAAGGCCCTCAGAGCCCTGCAGGAT
GCAATTCGACAGCTAGGAGGCATAGTGCGTGACGGAGAGAAGGTGGTGGAGATAAACCCA
GGGCTACTGGTCACGGTGAAAACCACCTCCAGGAGCTACCAAGCTAAGAGCTTGGTCATC
ACAGCAGGTCCTTGGACCAACCAGCTCCTCCGTCCCCTGGGCATTGAGATGCCTCTCCAG
ACCCTGCGGATCAACGTGTGTTACTGGCGAGAGATGGTTCCTGGGAGCTATGGTGTGTCC
CAGGCCTTTCCGTGCTTCCTGTGGCTGGGCTTGTGTCCCCACCACATCTACGGACTGCCC
ACAGGAGAGTACCCAGGGCTGATGAAGGTCAGCTATCACCACGGCAACCACGCAGACCCT
GAGGAGCGGGACTGCCCCACAGCACGCACAGACATCGGAGACGTCCAGATCCTGAGCAGC
TTTGTCAGAGATCACTTACCTGATCTGAAGCCCGAGCCTGCTGTCATTGAGAGCTGCATG
TACACGAATACCCCTGATGAGCAGTTCATTCTCGATCGCCACCCAAAGTATGACAACATT
GTCATTGGTGCTGGATTCTCTGGGCACGGGTTCAAGCTGGCCCCTGTGGTGGGGAAGATC
CTGTATGAATTAAGCATGAAATTAACACCATCTTATGACTTGGCACCTTTTCGAATCAGC
CGTTTCCCAAGCCTGGCCAAAGCCCACCTGTGA
Enzyme 1 GenBank Gene ID AF134593 Link Image
Enzyme 1 GeneCard ID PIPOX Link Image
Enzyme 1 GenAtlas ID PIPOX Link Image
Enzyme 1 HGNC ID HGNC:17804 Link Image
Enzyme 1 Chromosome Location 17
Enzyme 1 Locus 17q11.2
Enzyme 1 SNPs SNPJam Report Link Image
Enzyme 1 General References
  1. Dodt G, Kim DG, Reimann SA, Reuber BE, McCabe K, Gould SJ, Mihalik SJ: L-Pipecolic acid oxidase, a human enzyme essential for the degradation of L-pipecolic acid, is most similar to the monomeric sarcosine oxidases. Biochem J. 2000 Feb 1;345 Pt 3:487-94. [PubMed Link Image]
  2. Hu RM, Han ZG, Song HD, Peng YD, Huang QH, Ren SX, Gu YJ, Huang CH, Li YB, Jiang CL, Fu G, Zhang QH, Gu BW, Dai M, Mao YF, Gao GF, Rong R, Ye M, Zhou J, Xu SH, Gu J, Shi JX, Jin WR, Zhang CK, Wu TM, Huang GY, Chen Z, Chen MD, Chen JL: Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning. Proc Natl Acad Sci U S A. 2000 Aug 15;97(17):9543-8. [PubMed Link Image]
Enzyme 1 Metabolite References Not Available
Enzyme 2 [top]
Enzyme 2 ID 16475
Enzyme 2 Name cDNA FLJ14592 fis, clone NT2RM4002063, highly similar to Peroxisomal sarcosine oxidase (EC 1.5.3.1)
Enzyme 2 Synonyms
  1. SubName: Pipecolic acid oxidase, isoform CRA_b
Enzyme 2 Gene Name PIPOX
Enzyme 2 Protein Sequence >cDNA FLJ14592 fis, clone NT2RM4002063, highly similar to Peroxisomal sarcosine oxidase (EC 1.5.3.1) 
MAAQKDLWDAIVIGAGIQGCFTAYHLAKHRKRILLLEQFFLPHSRGSSHGQSRIIRKAYL
EDFYTRMMHECYQIWAQLEHEAGTQLHRQTGLLLLGMKENQELKTIQANLSRQRVEHQCL
SSEELKQRFPNIRLPRGEVGLLDNSGGVIYAYKALRALQDAIRQLGGIVRDGEKVVEINP
GLLVTVKTTSRSYQAKSLVITAGPWTNQLLRPLGIEMPLQTLRINVCYWREMVPGSYGVS
QAFPCFLWLGLCPHHIYGLPTGEYPGLMKVSYHHGNHADPEERDCPTARTDIGDVQILSS
FVRDHLPDLKPEPAVIESCMYTNTPDEQFILDRHPKYDNIVIGAGFSGHGFKLAPVVGKI
LYELSMKLTPSYDLAPFRISRFPSLGKAHL
Enzyme 2 Number of Residues 390
Enzyme 2 Molecular Weight 44067
Enzyme 2 Theoretical pI 8.54
Enzyme 2 GO Classification
Function
  • catalytic activity
  • oxidoreductase activity
  • oxidoreductase activity, acting on the CH-NH group of donors
  • oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor
  • sarcosine oxidase activity
Process
  • aromatic compound metabolism
  • cellular metabolism
  • electron transport
  • folic acid and derivative metabolism
  • generation of precursor metabolites and energy
  • metabolism
  • physiological process
  • tetrahydrofolate metabolism
Component
—
Enzyme 2 General Function Amino acid transport and metabolism
Enzyme 2 Specific Function Not Available
Enzyme 2 Pathways Not Available
Enzyme 2 Reactions
  • sarcosine + H2O + O2 = glycine + formaldehyde + H2O2 [RN:R00610] ALL_REAC R00610
Enzyme 2 Pfam Domain Function
Enzyme 2 Signals
  • None
Enzyme 2 Transmembrane Regions
  • None
Enzyme 2 Essentiality Not Available
Enzyme 2 GenBank ID Protein Not Available
Enzyme 2 UniProtKB/Swiss-Prot ID B3KNH0 Link Image
Enzyme 2 UniProtKB/Swiss-Prot Entry Name B3KNH0_HUMAN Link Image
Enzyme 2 PDB ID Not Available
Enzyme 2 Cellular Location Not Available
Enzyme 2 Gene Sequence Not Available
Enzyme 2 GenBank Gene ID AK027498 Link Image
Enzyme 2 GeneCard ID B3KNH0 Link Image
Enzyme 2 GenAtlas ID Not Available
Enzyme 2 HGNC ID Not Available
Enzyme 2 Chromosome Location 17
Enzyme 2 Locus 17q11.2
Enzyme 2 SNPs SNPJam Report Link Image
Enzyme 2 General References Not Available
Enzyme 2 Metabolite References Not Available