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Showing metabocard for 2,3,4,5-Tetrahydro-2-pyridinecarboxylic acid (HMDB0012130)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2009-04-06 16:19:43 UTC
Update Date2023-02-21 17:17:38 UTC
HMDB IDHMDB0012130
Secondary Accession Numbers
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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0012130 (2,3,4,5-Tetrahydro-2-pyridinecarboxylic acid)

  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
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3D MOL for HMDB0012130 (2,3,4,5-Tetrahydro-2-pyridinecarboxylic acid)

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
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3D SDF for HMDB0012130 (2,3,4,5-Tetrahydro-2-pyridinecarboxylic acid)

  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>
HMDB0012130

> <DATABASE_NAME>
hmdb

> <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

$$$$
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3D-SDF for HMDB0012130 (2,3,4,5-Tetrahydro-2-pyridinecarboxylic acid)

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
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PDB for HMDB0012130 (2,3,4,5-Tetrahydro-2-pyridinecarboxylic acid)

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
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3D PDB for HMDB0012130 (2,3,4,5-Tetrahydro-2-pyridinecarboxylic acid)

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
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SMILES for HMDB0012130 (2,3,4,5-Tetrahydro-2-pyridinecarboxylic acid)

OC(=O)[C@@H]1CCCC=N1
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INCHI for HMDB0012130 (2,3,4,5-Tetrahydro-2-pyridinecarboxylic acid)

InChI=1S/C6H9NO2/c8-6(9)5-3-1-2-4-7-5/h4-5H,1-3H2,(H,8,9)/t5-/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC6H9NO2
Average Molecular Weight127.1412
Monoisotopic Molecular Weight127.063328537
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
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids and derivatives
Alternative Parents
Substituents
  • Alpha-amino acid or derivatives
  • Tetrahydropyridine
  • Hydropyridine
  • Azacycle
  • Organoheterocyclic compound
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Organic oxide
  • Hydrocarbon derivative
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Imine
  • Carbonyl group
  • Organic nitrogen compound
  • Organopnictogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Not AvailableNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID21865623
KEGG Compound IDC00450
BioCyc IDCPD-7682
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound24771808
PDB IDNot Available
ChEBI ID49014
Food Biomarker OntologyNot Available
VMH IDTHP2C
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Peroxisomal sarcosine oxidase
General function:
Involved in oxidoreductase activity
Specific function:
Metabolizes sarcosine, L-pipecolic acid and L-proline.
Gene Name:
PIPOX
Uniprot ID:
Q9P0Z9
Molecular weight:
44065.515
Reactions
L-Pipecolic acid + Oxygen → 2,3,4,5-Tetrahydro-2-pyridinecarboxylic acid + Hydrogen peroxidedetails