Showing metabocard for 2,3,4,5-Tetrahydro-2-pyridinecarboxylic acid (MMDBc0047965)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-23 23:19:24 UTC
Update Date2024-04-30 20:33:58 UTC
Metabolite IDMMDBc0047965
Metabolite Identification
Common Name2,3,4,5-Tetrahydro-2-pyridinecarboxylic acid
Description2,3,4,5-Tetrahydro-2-pyridinecarboxylic acid (CAS: 3038-89-9), also known as 2,3,4,5-tetrahydropiperidine-2-carboxylate and 1-piperideine-6-carboxylic acid, is a cyclic intermediate in lysine degradation. L-Lysine is an essential amino acid that is a necessary building block for all protein in the body and It plays a major role in calcium absorption; building muscle protein; recovering from surgery or sports injuries; and the body's production of hormones, enzymes, and antibodies. In the lysine degradation pathway, 2,3,4,5-tetrahydro-2-pyridinecarboxylic acid is a substrate for L-aminoadipate-semialdehyde dehydrogenase (amaA) and can be formed by the spontaneous cyclization of 2-aminoadipate-6-semialdehyde. 2,3,4,5-Tetrahydro-2-pyridinecarboxylic acid is also an intermediate in glycine, serine, and threonine metabolism. It is a substrate for peroxisomal sarcosine oxidase.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9208a365c8>


  Mrv1652307191923512D          

  9  9  0  0  0  0            999 V2000
   -2.0758    0.2669    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7903   -0.1455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7903   -0.9706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0758   -1.3830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3613   -0.9706    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3613   -0.1455    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6469   -1.3831    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6469   -2.2081    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0675   -0.9707    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  7  1  6  0  0  0
  7  9  1  0  0  0  0
  7  8  2  0  0  0  0
  1  6  2  0  0  0  0
  5  6  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f9208a365c8>

HMDB0012130
     RDKit          3D
2,3,4,5-Tetrahydro-2-pyridinecarboxylic acid
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.5951    1.7824   -0.0259 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1542    0.6871    0.4056 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0630   -0.2700    0.8575 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7125    0.4313    0.4288 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3574   -0.8389   -0.3360 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1163   -0.9574   -0.5548 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9028    0.1787    0.0633 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2531    1.4552   -0.2650 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0050    1.5644   -0.0850 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8000   -1.2390    0.6710 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4049    0.2405    1.4833 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7498   -1.7008    0.2466 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9322   -0.8401   -1.2915 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3072   -1.0371   -1.6630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4817   -1.8989   -0.0548 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9985   -0.0076    1.1410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9262    0.1248   -0.3629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7882    2.3255   -0.6582 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  2  0
  9  4  1  0
  3 10  1  0
  4 11  1  1
  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
M  END
Download

3D SDF for #<Metabolite:0x00007f9208a365c8>


  Mrv1652307191923512D          

  9  9  0  0  0  0            999 V2000
   -2.0758    0.2669    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7903   -0.1455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7903   -0.9706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0758   -1.3830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3613   -0.9706    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3613   -0.1455    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6469   -1.3831    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6469   -2.2081    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0675   -0.9707    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  7  1  6  0  0  0
  7  9  1  0  0  0  0
  7  8  2  0  0  0  0
  1  6  2  0  0  0  0
  5  6  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0047965

> <DATABASE_NAME>
MIME

> <SMILES>
OC(=O)[C@@H]1CCCC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C6H9NO2/c8-6(9)5-3-1-2-4-7-5/h4-5H,1-3H2,(H,8,9)/t5-/m0/s1

> <INCHI_KEY>
CSDPVAKVEWETFG-YFKPBYRVSA-N

> <FORMULA>
C6H9NO2

> <MOLECULAR_WEIGHT>
127.1412

> <EXACT_MASS>
127.063328537

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.691354980800693

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2,3,4,5-tetrahydropyridine-2-carboxylic acid

> <ALOGPS_LOGP>
0.36

> <JCHEM_LOGP>
-1.8274562075723537

> <ALOGPS_LOGS>
-1.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.0027714730041635

> <JCHEM_PKA_STRONGEST_BASIC>
6.217105927847416

> <JCHEM_POLAR_SURFACE_AREA>
49.66

> <JCHEM_REFRACTIVITY>
31.9983

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.53e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2,3,4,5-tetrahydropyridine-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f9208a365c8>

HMDB0012130
     RDKit          3D
2,3,4,5-Tetrahydro-2-pyridinecarboxylic acid
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.5951    1.7824   -0.0259 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1542    0.6871    0.4056 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0630   -0.2700    0.8575 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7125    0.4313    0.4288 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3574   -0.8389   -0.3360 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1163   -0.9574   -0.5548 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9028    0.1787    0.0633 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2531    1.4552   -0.2650 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0050    1.5644   -0.0850 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8000   -1.2390    0.6710 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4049    0.2405    1.4833 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7498   -1.7008    0.2466 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9322   -0.8401   -1.2915 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3072   -1.0371   -1.6630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4817   -1.8989   -0.0548 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9985   -0.0076    1.1410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9262    0.1248   -0.3629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7882    2.3255   -0.6582 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  2  0
  9  4  1  0
  3 10  1  0
  4 11  1  1
  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
M  END
Download

PDB for #<Metabolite:0x00007f9208a365c8>

HEADER    PROTEIN                                 19-JUL-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-JUL-19         0                                  
HETATM    1  C   UNK     0      -3.875   0.498   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.209  -0.272   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.209  -1.812   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.875  -2.582   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.541  -1.812   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -2.541  -0.272   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -1.208  -2.582   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.208  -4.122   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.126  -1.812   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    7    6                                                  
CONECT    6    1    5                                                       
CONECT    7    5    9    8                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
Download

3D PDB for #<Metabolite:0x00007f9208a365c8>

COMPND    HMDB0012130
HETATM    1  O1  UNL     1       2.595   1.782  -0.026  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.154   0.687   0.406  1.00  0.00           C  
HETATM    3  O2  UNL     1       3.063  -0.270   0.857  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.712   0.431   0.429  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.357  -0.839  -0.336  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.116  -0.957  -0.555  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.903   0.179   0.063  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.253   1.455  -0.265  1.00  0.00           C  
HETATM    9  N1  UNL     1       0.005   1.564  -0.085  1.00  0.00           N  
HETATM   10  H1  UNL     1       2.800  -1.239   0.671  1.00  0.00           H  
HETATM   11  H2  UNL     1       0.405   0.240   1.483  1.00  0.00           H  
HETATM   12  H3  UNL     1       0.750  -1.701   0.247  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.932  -0.840  -1.292  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.307  -1.037  -1.663  1.00  0.00           H  
HETATM   15  H6  UNL     1      -1.482  -1.899  -0.055  1.00  0.00           H  
HETATM   16  H7  UNL     1      -1.998  -0.008   1.141  1.00  0.00           H  
HETATM   17  H8  UNL     1      -2.926   0.125  -0.363  1.00  0.00           H  
HETATM   18  H9  UNL     1      -1.788   2.326  -0.658  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    9   18
END
Download

SMILES for #<Metabolite:0x00007f9208a365c8>

OC(=O)[C@@H]1CCCC=N1
Download

INCHI for #<Metabolite:0x00007f9208a365c8>

InChI=1S/C6H9NO2/c8-6(9)5-3-1-2-4-7-5/h4-5H,1-3H2,(H,8,9)/t5-/m0/s1
Download
Synonyms
ValueSource
(S)-2,3,4,5-Tetrahydropyridine-2-carboxylic acidChEBI
delta1-Piperideine-6-L-carboxylateChEBI
Delta(1)-Piperideine-6-L-carboxylic acidChEBI
(S)-2,3,4,5-Tetrahydropyridine-2-carboxylateGenerator
delta1-Piperideine-6-L-carboxylic acidGenerator
Δ1-piperideine-6-L-carboxylateGenerator
Δ1-piperideine-6-L-carboxylic acidGenerator
delta(1)-Piperideine-6-L-carboxylateGenerator
Δ(1)-piperideine-6-L-carboxylateGenerator
Δ(1)-piperideine-6-L-carboxylic acidGenerator
2,3,4,5-Tetrahydro-2-pyridinecarboxylateGenerator
​2,3,4,5-tetrahydro-2-pyridinecarboxylateHMDB
(S)-1-Piperideine-6-carboxylateHMDB
(2S)-2,3,4,5-Tetrahydro-2-pyridinecarboxylic acidHMDB
(S)-2,3,4,5-Tetrahydro-2-pyridinecarboxylic acidHMDB
(S)-2,3,4,5-Tetrahydropiperidine-2-carboxylateHMDB
(S)-2,3,4,5-Tetrahydropiperidine-2-carboxylic acidHMDB
1-Piperideine-6-carboxylateHMDB
1-Piperideine-6-carboxylic acidHMDB
2,3,4,5-Tetrahydropicolinic acidHMDB
delta1-Piperideine-6-carboxylateHMDB
delta1-Piperideine-6-carboxylic acidHMDB
delta1-Piperidine-6-carboxylateHMDB
delta1-Piperidine-6-carboxylic acidHMDB
Δ1-piperidine-6-carboxylateHMDB
Δ1-piperidine-6-carboxylic acidHMDB
Δ1-piperideine-6-carboxylateHMDB
Δ1-piperideine-6-carboxylic acidHMDB
2,3,4,5-Tetrahydro-2-pyridinecarboxylic acidHMDB
Molecular FormulaC6H9NO2
Average Mass127.1412
Monoisotopic Mass127.063328537
IUPAC Name(2S)-2,3,4,5-tetrahydropyridine-2-carboxylic acid
Traditional Name(2S)-2,3,4,5-tetrahydropyridine-2-carboxylic acid
CAS Registry Number73980-78-6
SMILES
OC(=O)[C@@H]1CCCC=N1
InChI Identifier
InChI=1S/C6H9NO2/c8-6(9)5-3-1-2-4-7-5/h4-5H,1-3H2,(H,8,9)/t5-/m0/s1
InChI KeyCSDPVAKVEWETFG-YFKPBYRVSA-N