Showing metabocard for 1-Piperideine-2-carboxylic acid (MMDBc0047920)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-23 23:15:17 UTC
Update Date2022-09-01 02:01:36 UTC
Metabolite IDMMDBc0047920
Metabolite Identification
Common Name1-Piperideine-2-carboxylic acid
Description1-Piperideine-2-carboxylic acid (P2C), also known as Δ1-pipecolic acid, is classified as a member of the tetrahydropyridines. Tetrahydropyridines are derivatives of pyridine in which two double bonds in the pyridine moiety are reduced by adding four hydrogen atoms. 1-Piperideine-2-carboxylic acid is considered to be slightly soluble (in water) and acidic. 1-Piperideine-2-carboxylic acid is an intermediate of the L-lysine metabolic pathway in the brain; the uptake of P2C into the synaptosome of the cerebral cortex was Na+ and temperature-dependent (PMID: 7654748 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f262c50b438>


  Mrv1652305171818282D          

  9  9  0  0  0  0            999 V2000
    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
    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 N   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 C   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  2  0  0  0  0
  1  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  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  3  1  0  0  0  0
  9  1  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f262c50b438>

HMDB0001084
     RDKit          3D
1-Piperideine-2-carboxylic acid
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.3148   -1.5233    1.6658 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0967   -0.7481    0.6957 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1976   -0.2080    0.0603 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7455   -0.4427    0.2727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2478   -0.9419    0.8608 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6384   -0.7228    0.5437 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8305    0.2818   -0.5695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6974    1.2926   -0.5290 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5564    0.4739   -0.8720 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0929   -0.6779    0.0740 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2066   -0.3740    1.4315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1294   -1.6672    0.2100 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8276    0.7657   -0.5030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7097   -0.2545   -1.5479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8414    2.1242   -1.2111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6209    1.6086    0.5447 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3324   -0.1409   -1.7880 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4132    1.1545   -1.0350 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  2  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
  6 11  1  0
  6 12  1  0
  7 13  1  0
  7 14  1  0
  8 15  1  0
  8 16  1  0
  9 17  1  0
  9 18  1  0
M  END
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3D SDF for #<Metabolite:0x00007f262c50b438>


  Mrv1652305171818282D          

  9  9  0  0  0  0            999 V2000
    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
    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 N   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 C   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  2  0  0  0  0
  1  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  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  3  1  0  0  0  0
  9  1  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0047920

> <DATABASE_NAME>
MIME

> <SMILES>
OC(=O)C1=NCCCC1

> <INCHI_IDENTIFIER>
InChI=1S/C6H9NO2/c8-6(9)5-3-1-2-4-7-5/h1-4H2,(H,8,9)

> <INCHI_KEY>
GEJXSVNGWOSZPC-UHFFFAOYSA-N

> <FORMULA>
C6H9NO2

> <MOLECULAR_WEIGHT>
127.1412

> <EXACT_MASS>
127.063328537

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.836279738869656

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,4,5,6-tetrahydropyridine-2-carboxylic acid

> <ALOGPS_LOGP>
0.65

> <JCHEM_LOGP>
0.9737831613333332

> <ALOGPS_LOGS>
-1.39

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.088259725140425

> <JCHEM_PKA_STRONGEST_BASIC>
1.8931989193157819

> <JCHEM_POLAR_SURFACE_AREA>
49.660000000000004

> <JCHEM_REFRACTIVITY>
32.4398

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.18e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-piperideine-2-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f262c50b438>

HMDB0001084
     RDKit          3D
1-Piperideine-2-carboxylic acid
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.3148   -1.5233    1.6658 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0967   -0.7481    0.6957 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1976   -0.2080    0.0603 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7455   -0.4427    0.2727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2478   -0.9419    0.8608 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6384   -0.7228    0.5437 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8305    0.2818   -0.5695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6974    1.2926   -0.5290 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5564    0.4739   -0.8720 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0929   -0.6779    0.0740 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2066   -0.3740    1.4315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1294   -1.6672    0.2100 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8276    0.7657   -0.5030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7097   -0.2545   -1.5479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8414    2.1242   -1.2111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6209    1.6086    0.5447 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3324   -0.1409   -1.7880 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4132    1.1545   -1.0350 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  2  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
  6 11  1  0
  6 12  1  0
  7 13  1  0
  7 14  1  0
  8 15  1  0
  8 16  1  0
  9 17  1  0
  9 18  1  0
M  END
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PDB for #<Metabolite:0x00007f262c50b438>

HEADER    PROTEIN                                 17-MAY-18   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-MAY-18         0                                  
HETATM    1  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
CONECT    1    2    3    9                                                  
CONECT    2    1                                                            
CONECT    3    1    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    3                                                       
CONECT    9    1                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for #<Metabolite:0x00007f262c50b438>

COMPND    HMDB0001084
HETATM    1  O1  UNL     1       2.315  -1.523   1.666  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.097  -0.748   0.696  1.00  0.00           C  
HETATM    3  O2  UNL     1       3.198  -0.208   0.060  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.746  -0.443   0.273  1.00  0.00           C  
HETATM    5  N1  UNL     1      -0.248  -0.942   0.861  1.00  0.00           N  
HETATM    6  C3  UNL     1      -1.638  -0.723   0.544  1.00  0.00           C  
HETATM    7  C4  UNL     1      -1.831   0.282  -0.569  1.00  0.00           C  
HETATM    8  C5  UNL     1      -0.697   1.293  -0.529  1.00  0.00           C  
HETATM    9  C6  UNL     1       0.556   0.474  -0.872  1.00  0.00           C  
HETATM   10  H1  UNL     1       4.093  -0.678   0.074  1.00  0.00           H  
HETATM   11  H2  UNL     1      -2.207  -0.374   1.432  1.00  0.00           H  
HETATM   12  H3  UNL     1      -2.129  -1.667   0.210  1.00  0.00           H  
HETATM   13  H4  UNL     1      -2.828   0.766  -0.503  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.710  -0.254  -1.548  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.841   2.124  -1.211  1.00  0.00           H  
HETATM   16  H7  UNL     1      -0.621   1.609   0.545  1.00  0.00           H  
HETATM   17  H8  UNL     1       0.332  -0.141  -1.788  1.00  0.00           H  
HETATM   18  H9  UNL     1       1.413   1.155  -1.035  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   10
CONECT    4    5    5    9
CONECT    5    6
CONECT    6    7   11   12
CONECT    7    8   13   14
CONECT    8    9   15   16
CONECT    9   17   18
END
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SMILES for #<Metabolite:0x00007f262c50b438>

OC(=O)C1=NCCCC1
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INCHI for #<Metabolite:0x00007f262c50b438>

InChI=1S/C6H9NO2/c8-6(9)5-3-1-2-4-7-5/h1-4H2,(H,8,9)
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Synonyms
ValueSource
1,2-Didehydropiperidine-2-carboxylateChEBI
Delta(1)-Piperidine-2-carboxylic acidChEBI
1-Piperideine-2-carboxylateKegg
1,2-Didehydropiperidine-2-carboxylic acidGenerator
delta(1)-Piperidine-2-carboxylateGenerator
Δ(1)-piperidine-2-carboxylateGenerator
Δ(1)-piperidine-2-carboxylic acidGenerator
D-1-Piperideine-2-carboxylateHMDB
delta(1)-Piperideine-2-carboxylateHMDB
Delta1-Piperideine-2-carboxylateHMDB
1-p-2-CAHMDB
delta 1-Piperideine-2-carboxylateHMDB
delta1-Piperideine-2-carboxylic acidHMDB
Δ1-piperideine-2-carboxylateHMDB
Δ1-piperideine-2-carboxylic acidHMDB
3,4,5,6-Tetrahydro-2-pyridinecarboxylateHMDB
3,4,5,6-Tetrahydro-2-pyridinecarboxylic acidHMDB
D-1-Piperideine-2-carboxylic acidHMDB
delta1-Pipecolic acidHMDB
delta1-Piperidine-2-carboxylateHMDB
delta1-Piperidine-2-carboxylic acidHMDB
Δ1-pipecolic acidHMDB
Δ1-piperidine-2-carboxylateHMDB
Δ1-piperidine-2-carboxylic acidHMDB
P2CHMDB
1-Piperideine-2-carboxylic acidGenerator
Molecular FormulaC6H9NO2
Average Mass127.1412
Monoisotopic Mass127.063328537
IUPAC Name3,4,5,6-tetrahydropyridine-2-carboxylic acid
Traditional Name1-piperideine-2-carboxylate
CAS Registry Number2756-89-0
SMILES
OC(=O)C1=NCCCC1
InChI Identifier
InChI=1S/C6H9NO2/c8-6(9)5-3-1-2-4-7-5/h1-4H2,(H,8,9)
InChI KeyGEJXSVNGWOSZPC-UHFFFAOYSA-N