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Showing metabocard for 3-Succinoylpyridine (HMDB0000992)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:22 UTC
HMDB IDHMDB0000992
Secondary Accession Numbers
  • HMDB00992
Metabolite Identification
Common Name3-Succinoylpyridine
Description3-Succinoylpyridine, also known as 4-OPC4a, belongs to the class of organic compounds known as gamma-keto acids and derivatives. These are organic compounds containing an aldehyde substituted with a keto group on the C4 carbon atom. 3-Succinoylpyridine has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make 3-succinoylpyridine a potential biomarker for the consumption of these foods. 3-Succinoylpyridine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on 3-Succinoylpyridine.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000992 (3-Succinoylpyridine)

  Mrv0541 02231218512D          

 13 13  0  0  0  0            999 V2000
    8.4871   -7.4523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7659   -7.8645    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.4871   -6.6224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7659   -6.2217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0562   -7.4523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0562   -6.6281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1982   -6.2040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1914   -5.3791    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.9161   -6.6107    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6271   -6.1923    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3448   -6.5989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0559   -6.1806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.3516   -7.4239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  5  2  1  0  0  0  0
  4  3  2  0  0  0  0
  6  4  1  0  0  0  0
  6  5  2  0  0  0  0
  8  7  2  0  0  0  0
  9  7  1  0  0  0  0
  3  7  1  0  0  0  0
  9 10  1  0  0  0  0
 12 11  2  0  0  0  0
 13 11  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
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3D MOL for HMDB0000992 (3-Succinoylpyridine)

HMDB0000992
     RDKit          3D
3-Succinoylpyridine
 22 22  0  0  0  0  0  0  0  0999 V2000
    3.4035   -1.0933    1.3988 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4741   -0.1931    0.5317 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6391    0.5635    0.4225 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3171    0.0509   -0.3593 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1598   -0.8802    0.0336 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0515   -0.5924   -0.8670 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2182   -0.7210   -2.1322 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2518   -0.1614   -0.4122 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2529    0.0697   -1.3706 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5001    0.4900   -0.9928 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7133    0.6702    0.3586 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7566    0.4478    1.2679 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5151    0.0323    0.9226 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5668    1.5430    0.1208 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5197   -0.1561   -1.4169 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9714    1.0989   -0.1732 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9453   -0.7219    1.0725 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5664   -1.9185   -0.0929 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0553   -0.0814   -2.4410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3053    0.6784   -1.7215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7198    1.0105    0.6499 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7626   -0.1357    1.7078 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  2  0
  6  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13  8  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  9 19  1  0
 10 20  1  0
 11 21  1  0
 13 22  1  0
M  END
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3D SDF for HMDB0000992 (3-Succinoylpyridine)

  Mrv0541 02231218512D          

 13 13  0  0  0  0            999 V2000
    8.4871   -7.4523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7659   -7.8645    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.4871   -6.6224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7659   -6.2217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0562   -7.4523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0562   -6.6281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1982   -6.2040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1914   -5.3791    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.9161   -6.6107    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6271   -6.1923    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3448   -6.5989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0559   -6.1806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.3516   -7.4239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  5  2  1  0  0  0  0
  4  3  2  0  0  0  0
  6  4  1  0  0  0  0
  6  5  2  0  0  0  0
  8  7  2  0  0  0  0
  9  7  1  0  0  0  0
  3  7  1  0  0  0  0
  9 10  1  0  0  0  0
 12 11  2  0  0  0  0
 13 11  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000992

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)CCC(=O)C1=CC=CN=C1

> <INCHI_IDENTIFIER>
InChI=1S/C9H9NO3/c11-8(3-4-9(12)13)7-2-1-5-10-6-7/h1-2,5-6H,3-4H2,(H,12,13)

> <INCHI_KEY>
JGSUNMCABQUBOY-UHFFFAOYSA-N

> <FORMULA>
C9H9NO3

> <MOLECULAR_WEIGHT>
179.1727

> <EXACT_MASS>
179.058243159

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
17.556325354934724

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-oxo-4-(pyridin-3-yl)butanoic acid

> <ALOGPS_LOGP>
0.08

> <JCHEM_LOGP>
-0.5828774301236572

> <ALOGPS_LOGS>
-1.31

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
16.35802792230702

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.362515469149831

> <JCHEM_PKA_STRONGEST_BASIC>
4.003919475426097

> <JCHEM_POLAR_SURFACE_AREA>
67.26

> <JCHEM_REFRACTIVITY>
45.1972

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.78e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-succinoylpyridine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0000992 (3-Succinoylpyridine)

HMDB0000992
     RDKit          3D
3-Succinoylpyridine
 22 22  0  0  0  0  0  0  0  0999 V2000
    3.4035   -1.0933    1.3988 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4741   -0.1931    0.5317 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6391    0.5635    0.4225 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3171    0.0509   -0.3593 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1598   -0.8802    0.0336 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0515   -0.5924   -0.8670 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2182   -0.7210   -2.1322 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2518   -0.1614   -0.4122 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2529    0.0697   -1.3706 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5001    0.4900   -0.9928 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7133    0.6702    0.3586 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7566    0.4478    1.2679 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5151    0.0323    0.9226 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5668    1.5430    0.1208 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5197   -0.1561   -1.4169 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9714    1.0989   -0.1732 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9453   -0.7219    1.0725 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5664   -1.9185   -0.0929 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0553   -0.0814   -2.4410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3053    0.6784   -1.7215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7198    1.0105    0.6499 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7626   -0.1357    1.7078 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  2  0
  6  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13  8  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  9 19  1  0
 10 20  1  0
 11 21  1  0
 13 22  1  0
M  END
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PDB for HMDB0000992 (3-Succinoylpyridine)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      15.843 -13.911   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      14.496 -14.680   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      15.843 -12.362   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      14.496 -11.614   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      13.172 -13.911   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      13.172 -12.372   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      17.170 -11.581   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      17.157 -10.041   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      18.510 -12.340   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      19.837 -11.559   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      21.177 -12.318   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      22.504 -11.537   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      21.190 -13.858   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    5                                                       
CONECT    3    1    4    7                                                  
CONECT    4    3    6                                                       
CONECT    5    2    6                                                       
CONECT    6    4    5                                                       
CONECT    7    8    9    3                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   12   13   10                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END
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3D PDB for HMDB0000992 (3-Succinoylpyridine)

COMPND    HMDB0000992
HETATM    1  O1  UNL     1       3.404  -1.093   1.399  1.00  0.00           O  
HETATM    2  C1  UNL     1       3.474  -0.193   0.532  1.00  0.00           C  
HETATM    3  O2  UNL     1       4.639   0.563   0.422  1.00  0.00           O  
HETATM    4  C2  UNL     1       2.317   0.051  -0.359  1.00  0.00           C  
HETATM    5  C3  UNL     1       1.160  -0.880   0.034  1.00  0.00           C  
HETATM    6  C4  UNL     1       0.051  -0.592  -0.867  1.00  0.00           C  
HETATM    7  O3  UNL     1       0.218  -0.721  -2.132  1.00  0.00           O  
HETATM    8  C5  UNL     1      -1.252  -0.161  -0.412  1.00  0.00           C  
HETATM    9  C6  UNL     1      -2.253   0.070  -1.371  1.00  0.00           C  
HETATM   10  C7  UNL     1      -3.500   0.490  -0.993  1.00  0.00           C  
HETATM   11  C8  UNL     1      -3.713   0.670   0.359  1.00  0.00           C  
HETATM   12  N1  UNL     1      -2.757   0.448   1.268  1.00  0.00           N  
HETATM   13  C9  UNL     1      -1.515   0.032   0.923  1.00  0.00           C  
HETATM   14  H1  UNL     1       4.567   1.543   0.121  1.00  0.00           H  
HETATM   15  H2  UNL     1       2.520  -0.156  -1.417  1.00  0.00           H  
HETATM   16  H3  UNL     1       1.971   1.099  -0.173  1.00  0.00           H  
HETATM   17  H4  UNL     1       0.945  -0.722   1.072  1.00  0.00           H  
HETATM   18  H5  UNL     1       1.566  -1.918  -0.093  1.00  0.00           H  
HETATM   19  H6  UNL     1      -2.055  -0.081  -2.441  1.00  0.00           H  
HETATM   20  H7  UNL     1      -4.305   0.678  -1.721  1.00  0.00           H  
HETATM   21  H8  UNL     1      -4.720   1.010   0.650  1.00  0.00           H  
HETATM   22  H9  UNL     1      -0.763  -0.136   1.708  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   14
CONECT    4    5   15   16
CONECT    5    6   17   18
CONECT    6    7    7    8
CONECT    8    9    9   13
CONECT    9   10   19
CONECT   10   11   11   20
CONECT   11   12   21
CONECT   12   13   13
CONECT   13   22
END
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SMILES for HMDB0000992 (3-Succinoylpyridine)

OC(=O)CCC(=O)C1=CC=CN=C1
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INCHI for HMDB0000992 (3-Succinoylpyridine)

InChI=1S/C9H9NO3/c11-8(3-4-9(12)13)7-2-1-5-10-6-7/h1-2,5-6H,3-4H2,(H,12,13)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC9H9NO3
Average Molecular Weight179.1727
Monoisotopic Molecular Weight179.058243159
IUPAC Name4-oxo-4-(pyridin-3-yl)butanoic acid
Traditional Name3-succinoylpyridine
CAS Registry Number4192-31-8
SMILES
OC(=O)CCC(=O)C1=CC=CN=C1
InChI Identifier
InChI=1S/C9H9NO3/c11-8(3-4-9(12)13)7-2-1-5-10-6-7/h1-2,5-6H,3-4H2,(H,12,13)
InChI KeyJGSUNMCABQUBOY-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as gamma-keto acids and derivatives. These are organic compounds containing an aldehyde substituted with a keto group on the C4 carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassKeto acids and derivatives
Sub ClassGamma-keto acids and derivatives
Direct ParentGamma-keto acids and derivatives
Alternative Parents
Substituents
  • Gamma-keto acid
  • Aryl ketone
  • Aryl alkyl ketone
  • Pyridine
  • Heteroaromatic compound
  • Ketone
  • Azacycle
  • Organoheterocyclic compound
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot 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 IDFDB022355
KNApSAcK IDNot Available
Chemspider ID424
KEGG Compound IDC19569
BioCyc IDCPD-14094
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5924
PubChem Compound437
PDB IDNot Available
ChEBI ID66951
Food Biomarker OntologyNot Available
VMH IDM00917
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceSchwartz, Sorell L.; McKennis, Herbert, Jr. The degradation of the pyrrolidine ring of (-)-nicotine in vitro. Formation of g-(3-pyridyl)-g-oxobutyric acid. Journal of Biological Chemistry (1963), 238 1807-12.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Felicia ND, Rekha GK, Murphy SE: Characterization of cytochrome P450 2A4 and 2A5-catalyzed 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) metabolism. Arch Biochem Biophys. 2000 Dec 15;384(2):418-24. [PubMed:11368333 ]
  2. Baidoo EE, Clench MR, Smith RF, Tetler LW: Determination of nicotine and its metabolites in urine by solid-phase extraction and sample stacking capillary electrophoresis-mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Nov 5;796(2):303-13. [PubMed:14581070 ]