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Showing metabocard for L-Pipecolic acid (HMDB0000716)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2022-09-22 17:43:44 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000716 (L-Pipecolic acid)

  Mrv1652309272007402D          

  9  9  0  0  1  0            999 V2000
   -3.3031    0.8705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0176    0.4580    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3031    1.6955    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5887    0.4580    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7321   -0.7795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4466   -0.3670    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4466    0.4580    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7321    0.8704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0176   -0.3670    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  2  0  0  0  0
  1  4  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  2  1  0  0  0  0
  5  9  1  0  0  0  0
  2  9  1  0  0  0  0
  2  1  1  1  0  0  0
M  END
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3D MOL for HMDB0000716 (L-Pipecolic acid)

HMDB0000716
     RDKit          3D
L-Pipecolic acid
 20 20  0  0  0  0  0  0  0  0999 V2000
    3.1462   -0.3823   -0.7555 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0368   -0.1032   -0.2157 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1157    0.4107    1.0802 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7324   -0.2771   -0.9225 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0593    0.9988   -0.9304 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7848    1.2694    0.3527 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1962    0.0291    1.0902 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2746   -1.1200    0.1185 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0190   -1.4163   -0.4309 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3717   -0.1628    1.8852 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9969   -0.4884   -1.9907 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6733    1.8302   -1.0901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7185    1.0178   -1.8268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1380    1.8619    1.0178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6936    1.8695    0.1041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1451    0.1425    1.6511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4317   -0.2523    1.8536 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5712   -2.0156    0.7221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0617   -0.9893   -0.6395 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0174   -2.2225   -1.0732 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9  4  1  0
  3 10  1  0
  4 11  1  6
  5 12  1  0
  5 13  1  0
  6 14  1  0
  6 15  1  0
  7 16  1  0
  7 17  1  0
  8 18  1  0
  8 19  1  0
  9 20  1  0
M  END
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3D SDF for HMDB0000716 (L-Pipecolic acid)

  Mrv1652309272007402D          

  9  9  0  0  1  0            999 V2000
   -3.3031    0.8705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0176    0.4580    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3031    1.6955    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5887    0.4580    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7321   -0.7795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4466   -0.3670    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4466    0.4580    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7321    0.8704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0176   -0.3670    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  2  0  0  0  0
  1  4  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  2  1  0  0  0  0
  5  9  1  0  0  0  0
  2  9  1  0  0  0  0
  2  1  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0000716

> <DATABASE_NAME>
hmdb

> <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_KEY>
HXEACLLIILLPRG-YFKPBYRVSA-N

> <FORMULA>
C6H11NO2

> <MOLECULAR_WEIGHT>
129.157

> <EXACT_MASS>
129.078978601

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.489921399346262

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-piperidine-2-carboxylic acid

> <ALOGPS_LOGP>
-2.17

> <JCHEM_LOGP>
-2.1239620485400845

> <ALOGPS_LOGS>
0.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.063103444066459

> <JCHEM_PKA_STRONGEST_BASIC>
10.388033490366288

> <JCHEM_POLAR_SURFACE_AREA>
49.33

> <JCHEM_REFRACTIVITY>
32.6653

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.58e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-pipecolic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0000716 (L-Pipecolic acid)

HMDB0000716
     RDKit          3D
L-Pipecolic acid
 20 20  0  0  0  0  0  0  0  0999 V2000
    3.1462   -0.3823   -0.7555 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0368   -0.1032   -0.2157 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1157    0.4107    1.0802 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7324   -0.2771   -0.9225 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0593    0.9988   -0.9304 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7848    1.2694    0.3527 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1962    0.0291    1.0902 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2746   -1.1200    0.1185 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0190   -1.4163   -0.4309 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3717   -0.1628    1.8852 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9969   -0.4884   -1.9907 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6733    1.8302   -1.0901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7185    1.0178   -1.8268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1380    1.8619    1.0178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6936    1.8695    0.1041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1451    0.1425    1.6511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4317   -0.2523    1.8536 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5712   -2.0156    0.7221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0617   -0.9893   -0.6395 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0174   -2.2225   -1.0732 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9  4  1  0
  3 10  1  0
  4 11  1  6
  5 12  1  0
  5 13  1  0
  6 14  1  0
  6 15  1  0
  7 16  1  0
  7 17  1  0
  8 18  1  0
  8 19  1  0
  9 20  1  0
M  END
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PDB for HMDB0000716 (L-Pipecolic acid)

HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  C   UNK     0      -6.166   1.625   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -7.500   0.855   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -6.166   3.165   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      -4.832   0.855   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -8.833  -1.455   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0     -10.167  -0.685   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0     -10.167   0.855   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -8.833   1.625   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -7.500  -0.685   0.000  0.00  0.00           N+0
CONECT    1    3    4    2                                                  
CONECT    2    8    9    1                                                  
CONECT    3    1                                                            
CONECT    4    1                                                            
CONECT    5    6    9                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    2                                                       
CONECT    9    5    2                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for HMDB0000716 (L-Pipecolic acid)

COMPND    HMDB0000716
HETATM    1  O1  UNL     1       3.146  -0.382  -0.756  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.037  -0.103  -0.216  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.116   0.411   1.080  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.732  -0.277  -0.922  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.059   0.999  -0.930  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.785   1.269   0.353  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.196   0.029   1.090  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.275  -1.120   0.119  1.00  0.00           C  
HETATM    9  N1  UNL     1       0.019  -1.416  -0.431  1.00  0.00           N  
HETATM   10  H1  UNL     1       2.372  -0.163   1.885  1.00  0.00           H  
HETATM   11  H2  UNL     1       0.997  -0.488  -1.991  1.00  0.00           H  
HETATM   12  H3  UNL     1       0.673   1.830  -1.090  1.00  0.00           H  
HETATM   13  H4  UNL     1      -0.719   1.018  -1.827  1.00  0.00           H  
HETATM   14  H5  UNL     1      -0.138   1.862   1.018  1.00  0.00           H  
HETATM   15  H6  UNL     1      -1.694   1.869   0.104  1.00  0.00           H  
HETATM   16  H7  UNL     1      -2.145   0.142   1.651  1.00  0.00           H  
HETATM   17  H8  UNL     1      -0.432  -0.252   1.854  1.00  0.00           H  
HETATM   18  H9  UNL     1      -1.571  -2.016   0.722  1.00  0.00           H  
HETATM   19  H10 UNL     1      -2.062  -0.989  -0.640  1.00  0.00           H  
HETATM   20  H11 UNL     1      -0.017  -2.222  -1.073  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   10
CONECT    4    5    9   11
CONECT    5    6   12   13
CONECT    6    7   14   15
CONECT    7    8   16   17
CONECT    8    9   18   19
CONECT    9   20
END
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SMILES for HMDB0000716 (L-Pipecolic acid)

OC(=O)[C@@H]1CCCCN1
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INCHI for HMDB0000716 (L-Pipecolic acid)

InChI=1S/C6H11NO2/c8-6(9)5-3-1-2-4-7-5/h5,7H,1-4H2,(H,8,9)/t5-/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
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
Biological locationRoute of exposureSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point272 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility74060 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Baker133.81530932474
[M-H]-MetCCS_train_neg126.71330932474
[M+H]+Baker130.93330932474
[M+H]+MetCCS_train_pos127.40230932474
[M-H]-Not Available128.6http://allccs.zhulab.cn/database/detail?ID=AllCCS00000028
[M+H]+Not Available128.4http://allccs.zhulab.cn/database/detail?ID=AllCCS00000028
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Peroxisome
Biospecimen Locations
  • Blood
  • Feces
  • Urine
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
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation 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
Good Scents IDrw1253961
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)Not Available
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

Enzyme Details
1. Peroxisomal sarcosine oxidase
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