Showing metabocard for N-Methylpipecolate (MMDBc0000833)

Record Information
Version2.0
StatusDetected and Quantified
Creation Date2020-12-10 23:04:49 UTC
Update Date2025-10-07 16:04:22 UTC
Metabolite IDMMDBc0000833
Metabolite Identification
Common NameN-Methylpipecolate
DescriptionN-Methylpipecolate is a metabolite classified as an amino acid derivative. Its chemical structure features a piperidine ring with a methyl group attached to the nitrogen, contributing to its unique properties. N-Methylpipecolate is involved in various metabolic pathways, including those related to amino acid metabolism and the regulation of nervous system functions. Notably, it may mediate the causal effect of N6,N6-dimethyllysine on anxious personality disorder, as indicated by studies suggesting its role in the metabolic pathways influencing mental health (PMID:40155430 , PMID:37425837 ). Additionally, it has been identified as a significant metabolite associated with kidney function and is part of a broader metabolic profile linked to dietary intake, particularly from navy beans (PMID:31720858 , PMID:30583518 ). The consumption of dietary betaine has been shown to impact levels of N-methylpipecolate, among other metabolites, highlighting its connection to dietary influences on metabolism (PMID:35327165 ). Overall, N-Methylpipecolate serves as an important compound in various biochemical contexts, reflecting its potential implications in both health and disease.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9aaa1b3608>


  Mrv1652312112000042D          

 10 10  0  0  1  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   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 C   0  0  2  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 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    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
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  6  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f9aaa1b3608>

HMDB0242107
     RDKit          3D
(R)-1-Methylpiperidine-2-carboxylic acid
 23 23  0  0  0  0  0  0  0  0999 V2000
    1.1698    1.8644   -0.6604 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5115    0.7748   -0.0251 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5653    1.0641    0.8050 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7948    0.2480    0.6741 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5703   -1.1749    0.2754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6542   -1.2054   -0.9085 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6393   -0.4860   -0.6148 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5788   -1.3859    0.1466 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7785   -2.5516   -0.2847 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1716   -0.8833    1.2788 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2630    1.7988   -0.4041 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0471    1.7615   -1.7534 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7206    2.8221   -0.3563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8645    2.1452    0.6620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2247    1.0306    1.8821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4722    0.7047   -0.1036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3371    0.2471    1.6432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5594   -1.5787   -0.0694 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2296   -1.8311    1.0852 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4007   -2.2279   -1.2149 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1491   -0.6770   -1.7489 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1401   -0.3601   -1.6216 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8015   -0.0995    1.3136 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  7  2  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
  6 20  1  0
  6 21  1  0
  7 22  1  6
 10 23  1  0
M  END
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3D SDF for #<Metabolite:0x00007f9aaa1b3608>


  Mrv1652312112000042D          

 10 10  0  0  1  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   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 C   0  0  2  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 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    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
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  6  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000833

> <DATABASE_NAME>
MIME

> <SMILES>
CN1CCCC[C@@H]1C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H13NO2/c1-8-5-3-2-4-6(8)7(9)10/h6H,2-5H2,1H3,(H,9,10)/t6-/m1/s1

> <INCHI_KEY>
BPSLZWSRHTULGU-ZCFIWIBFSA-N

> <FORMULA>
C7H13NO2

> <MOLECULAR_WEIGHT>
143.186

> <EXACT_MASS>
143.094628663

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.409081798930723

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-1-methylpiperidine-2-carboxylic acid

> <ALOGPS_LOGP>
-1.63

> <JCHEM_LOGP>
-1.9998375087357816

> <ALOGPS_LOGS>
0.46

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8596274243687096

> <JCHEM_PKA_STRONGEST_BASIC>
10.15297157381098

> <JCHEM_POLAR_SURFACE_AREA>
40.540000000000006

> <JCHEM_REFRACTIVITY>
37.96

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.14e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-1-methylpiperidine-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f9aaa1b3608>

HMDB0242107
     RDKit          3D
(R)-1-Methylpiperidine-2-carboxylic acid
 23 23  0  0  0  0  0  0  0  0999 V2000
    1.1698    1.8644   -0.6604 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5115    0.7748   -0.0251 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5653    1.0641    0.8050 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7948    0.2480    0.6741 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5703   -1.1749    0.2754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6542   -1.2054   -0.9085 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6393   -0.4860   -0.6148 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5788   -1.3859    0.1466 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7785   -2.5516   -0.2847 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1716   -0.8833    1.2788 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2630    1.7988   -0.4041 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0471    1.7615   -1.7534 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7206    2.8221   -0.3563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8645    2.1452    0.6620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2247    1.0306    1.8821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4722    0.7047   -0.1036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3371    0.2471    1.6432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5594   -1.5787   -0.0694 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2296   -1.8311    1.0852 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4007   -2.2279   -1.2149 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1491   -0.6770   -1.7489 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1401   -0.3601   -1.6216 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8015   -0.0995    1.3136 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  7  2  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
  6 20  1  0
  6 21  1  0
  7 22  1  6
 10 23  1  0
M  END
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PDB for #<Metabolite:0x00007f9aaa1b3608>

HEADER    PROTEIN                                 11-DEC-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-DEC-20         0                                  
HETATM    1  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    2    8                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for #<Metabolite:0x00007f9aaa1b3608>

COMPND    HMDB0242107
HETATM    1  C1  UNL     1       1.170   1.864  -0.660  1.00  0.00           C  
HETATM    2  N1  UNL     1       0.511   0.775  -0.025  1.00  0.00           N  
HETATM    3  C2  UNL     1      -0.565   1.064   0.805  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.795   0.248   0.674  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.570  -1.175   0.275  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.654  -1.205  -0.909  1.00  0.00           C  
HETATM    7  C6  UNL     1       0.639  -0.486  -0.615  1.00  0.00           C  
HETATM    8  C7  UNL     1       1.579  -1.386   0.147  1.00  0.00           C  
HETATM    9  O1  UNL     1       1.778  -2.552  -0.285  1.00  0.00           O  
HETATM   10  O2  UNL     1       2.172  -0.883   1.279  1.00  0.00           O  
HETATM   11  H1  UNL     1       2.263   1.799  -0.404  1.00  0.00           H  
HETATM   12  H2  UNL     1       1.047   1.762  -1.753  1.00  0.00           H  
HETATM   13  H3  UNL     1       0.721   2.822  -0.356  1.00  0.00           H  
HETATM   14  H4  UNL     1      -0.864   2.145   0.662  1.00  0.00           H  
HETATM   15  H5  UNL     1      -0.225   1.031   1.882  1.00  0.00           H  
HETATM   16  H6  UNL     1      -2.472   0.705  -0.104  1.00  0.00           H  
HETATM   17  H7  UNL     1      -2.337   0.247   1.643  1.00  0.00           H  
HETATM   18  H8  UNL     1      -2.559  -1.579  -0.069  1.00  0.00           H  
HETATM   19  H9  UNL     1      -1.230  -1.831   1.085  1.00  0.00           H  
HETATM   20  H10 UNL     1      -0.401  -2.228  -1.215  1.00  0.00           H  
HETATM   21  H11 UNL     1      -1.149  -0.677  -1.749  1.00  0.00           H  
HETATM   22  H12 UNL     1       1.140  -0.360  -1.622  1.00  0.00           H  
HETATM   23  H13 UNL     1       2.801  -0.099   1.314  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3    7
CONECT    3    4   14   15
CONECT    4    5   16   17
CONECT    5    6   18   19
CONECT    6    7   20   21
CONECT    7    8   22
CONECT    8    9    9   10
CONECT   10   23
END
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SMILES for #<Metabolite:0x00007f9aaa1b3608>

CN1CCCC[C@@H]1C(O)=O
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INCHI for #<Metabolite:0x00007f9aaa1b3608>

InChI=1S/C7H13NO2/c1-8-5-3-2-4-6(8)7(9)10/h6H,2-5H2,1H3,(H,9,10)/t6-/m1/s1
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Synonyms
ValueSource
(R)-1-Methylpiperidine-2-carboxylateGenerator
Molecular FormulaC7H13NO2
Average Mass143.186
Monoisotopic Mass143.094628663
IUPAC Name(2R)-1-methylpiperidine-2-carboxylic acid
Traditional Name(2R)-1-methylpiperidine-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
CN1CCCC[C@@H]1C(O)=O
InChI Identifier
InChI=1S/C7H13NO2/c1-8-5-3-2-4-6(8)7(9)10/h6H,2-5H2,1H3,(H,9,10)/t6-/m1/s1
InChI KeyBPSLZWSRHTULGU-ZCFIWIBFSA-N