Showing metabocard for Pipecolic acid (MMDBc0000492)

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Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:39:00 UTC
Update Date2024-04-30 19:32:37 UTC
Metabolite IDMMDBc0000492
Metabolite 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.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000555d2e1e6398>

  Mrv1652305201901062D          

  9  9  0  0  0  0            999 V2000
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  7  1  0  0  0  0
  7  8  2  0  0  0  0
  6  1  1  0  0  0  0
  9  7  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x0000555d2e1e6398>

HMDB0000070
     RDKit          3D
Pipecolic acid
 20 20  0  0  0  0  0  0  0  0999 V2000
    2.7271    1.3582   -0.5772 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2722    0.2354   -0.2054 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1517   -0.8255   -0.1684 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8562    0.0986    0.1665 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2186   -0.8442   -0.8638 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2673   -0.8897   -0.6662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7506   -0.1065    0.5091 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1283    1.2334    0.6678 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1651    1.3520    0.0393 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9514   -1.5955    0.4624 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7203   -0.2702    1.1856 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7043   -1.8199   -0.8247 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3869   -0.3179   -1.8491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5556   -1.9586   -0.5186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8385   -0.5647   -1.5766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6728   -0.7586    1.4059 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8586    0.0486    0.3637 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7778    2.0293    0.2558 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9853    1.4305    1.7691 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6809    2.1653    0.4247 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  0
  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:0x0000555d2e1e6398>

  Mrv1652305201901062D          

  9  9  0  0  0  0            999 V2000
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  7  1  0  0  0  0
  7  8  2  0  0  0  0
  6  1  1  0  0  0  0
  9  7  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000492

> <DATABASE_NAME>
MIME

> <SMILES>
OC(=O)C1CCCCN1

> <INCHI_IDENTIFIER>
InChI=1S/C6H11NO2/c8-6(9)5-3-1-2-4-7-5/h5,7H,1-4H2,(H,8,9)

> <INCHI_KEY>
HXEACLLIILLPRG-UHFFFAOYSA-N

> <FORMULA>
C6H11NO2

> <MOLECULAR_WEIGHT>
129.157

> <EXACT_MASS>
129.078978601

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.474269717299649

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
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>
(+,-)-pipecolic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x0000555d2e1e6398>

HMDB0000070
     RDKit          3D
Pipecolic acid
 20 20  0  0  0  0  0  0  0  0999 V2000
    2.7271    1.3582   -0.5772 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2722    0.2354   -0.2054 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1517   -0.8255   -0.1684 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8562    0.0986    0.1665 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2186   -0.8442   -0.8638 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2673   -0.8897   -0.6662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7506   -0.1065    0.5091 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1283    1.2334    0.6678 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1651    1.3520    0.0393 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9514   -1.5955    0.4624 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7203   -0.2702    1.1856 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7043   -1.8199   -0.8247 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3869   -0.3179   -1.8491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5556   -1.9586   -0.5186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8385   -0.5647   -1.5766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6728   -0.7586    1.4059 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8586    0.0486    0.3637 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7778    2.0293    0.2558 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9853    1.4305    1.7691 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6809    2.1653    0.4247 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  0
  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:0x0000555d2e1e6398>

HEADER    PROTEIN                                 20-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAY-19         0                                  
HETATM    1  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
CONECT    1    2    7    6                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
CONECT    7    1    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for #<Metabolite:0x0000555d2e1e6398>

COMPND    HMDB0000070
HETATM    1  O1  UNL     1       2.727   1.358  -0.577  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.272   0.235  -0.205  1.00  0.00           C  
HETATM    3  O2  UNL     1       3.152  -0.825  -0.168  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.856   0.099   0.167  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.219  -0.844  -0.864  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.267  -0.890  -0.666  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.751  -0.106   0.509  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.128   1.233   0.668  1.00  0.00           C  
HETATM    9  N1  UNL     1       0.165   1.352   0.039  1.00  0.00           N  
HETATM   10  H1  UNL     1       2.951  -1.595   0.462  1.00  0.00           H  
HETATM   11  H2  UNL     1       0.720  -0.270   1.186  1.00  0.00           H  
HETATM   12  H3  UNL     1       0.704  -1.820  -0.825  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.387  -0.318  -1.849  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.556  -1.959  -0.519  1.00  0.00           H  
HETATM   15  H6  UNL     1      -1.838  -0.565  -1.577  1.00  0.00           H  
HETATM   16  H7  UNL     1      -1.673  -0.759   1.406  1.00  0.00           H  
HETATM   17  H8  UNL     1      -2.859   0.049   0.364  1.00  0.00           H  
HETATM   18  H9  UNL     1      -1.778   2.029   0.256  1.00  0.00           H  
HETATM   19  H10 UNL     1      -0.985   1.430   1.769  1.00  0.00           H  
HETATM   20  H11 UNL     1       0.681   2.165   0.425  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:0x0000555d2e1e6398>

OC(=O)C1CCCCN1
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INCHI for #<Metabolite:0x0000555d2e1e6398>

InChI=1S/C6H11NO2/c8-6(9)5-3-1-2-4-7-5/h5,7H,1-4H2,(H,8,9)
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Synonyms
Molecular FormulaC6H11NO2
Average Mass129.157
Monoisotopic Mass129.078978601
IUPAC Namepiperidine-2-carboxylic acid
Traditional Name(+,-)-pipecolic acid
CAS Registry NumberNot Available
SMILES
OC(=O)C1CCCCN1
InChI Identifier
InChI=1S/C6H11NO2/c8-6(9)5-3-1-2-4-7-5/h5,7H,1-4H2,(H,8,9)
InChI KeyHXEACLLIILLPRG-UHFFFAOYSA-N