Showing metabocard for L-Pipecolic acid (MMDBc0047912)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-23 23:14:40 UTC
Update Date2024-04-30 20:32:20 UTC
Metabolite IDMMDBc0047912
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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007feca6110bd0>


  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 #<Metabolite:0x00007feca6110bd0>

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 #<Metabolite:0x00007feca6110bd0>


  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>
MMDBc0047912

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00007feca6110bd0>

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 #<Metabolite:0x00007feca6110bd0>

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 #<Metabolite:0x00007feca6110bd0>

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 #<Metabolite:0x00007feca6110bd0>

OC(=O)[C@@H]1CCCCN1
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INCHI for #<Metabolite:0x00007feca6110bd0>

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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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 acidHMDB
(-)-Pipecolinic acidHMDB
(2S)-Piperidine-2-carboxylic acidHMDB
(RS)-2-Piperidinecarboxylic acidHMDB
(±)-2-piperidinecarboxylic acidHMDB
(±)-pipecolic acidHMDB
(±)-pipecolinic acidHMDB
2-CarboxypiperidineHMDB
2-Pipecolinic acidHMDB
2-Piperidinylcarboxylic acidHMDB
DL-2-Piperidinecarboxylic acidHMDB
DL-Pipecolic acidHMDB
DL-Pipecolinic acidHMDB
DihydrobaikianeHMDB
Hexahydro-2-picolinic acidHMDB
HomoprolineHMDB
Piperidine-6-carboxylic acidHMDB
Piperolinic acidHMDB
alpha-Pipecolinic acidHMDB
Α-pipecolinic acidHMDB
L-Pipecolic acidPhytoBank
Molecular FormulaC6H11NO2
Average Mass129.157
Monoisotopic Mass129.078978601
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