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Showing metabocard for 3-Pyridylacetic acid (HMDB0001538)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:46 UTC
HMDB IDHMDB0001538
Secondary Accession Numbers
  • HMDB01538
Metabolite Identification
Common Name3-Pyridylacetic acid
Description3-Pyridylacetic acid is a breakdown product of nicotine (and other tobacco alkaloids) and is part of the nicotine degradation pathway. It is formed from 4-(3-pyridyl)-butanoate. One alkaloid in particular, myosmine, appears to be a major source for 3-pyridylacetic acid. The alkaloid myosmine is present not only in tobacco products but also in various foods. Myosmine is easily nitrosated, yielding 4-hydroxy-1-(3-pyridyl)-1-butanone (HPB) and the esophageal tobacco carcinogen N'-nitrosonornicotine. The two major metabolites of myosmine metabolism have been identified as 3-pyridylacetic acid (20-26%) and 4-oxo-4-(3-pyridyl)butyric acid (50-60%) (PMID:16079272 ). 3-pyridylacetatic acid is an analog of nicotinic acid. (PMID 13898750 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001538 (3-Pyridylacetic acid)

  Mrv1652305261923582D          

 10 10  0  0  0  0            999 V2000
   11.5275   -5.8963    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5275   -6.7250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.2462   -5.4910    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.8342   -5.4812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1133   -5.8823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4055   -5.4584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1002   -6.7072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6846   -5.8596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3793   -7.1083    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.6715   -6.6845    0.0000 C   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
  4  1  1  0  0  0  0
  6  5  1  0  0  0  0
  7  5  2  0  0  0  0
  8  6  2  0  0  0  0
  9  7  1  0  0  0  0
 10  8  1  0  0  0  0
 10  9  2  0  0  0  0
  4  5  1  0  0  0  0
M  END
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3D MOL for HMDB0001538 (3-Pyridylacetic acid)

HMDB0001538
     RDKit          3D
3-Pyridylacetic acid
 17 17  0  0  0  0  0  0  0  0999 V2000
   -1.8230    1.4794   -0.1379 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2442    0.2945   -0.1227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5705   -0.0236   -0.2781 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2495   -0.8058    0.0734 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1215   -0.2736    0.2220 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9236   -0.0934   -0.8950 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2042    0.4042   -0.7528 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7016    0.7281    0.5014 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8942    0.5383    1.5485 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6482    0.0593    1.4566 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8443   -0.6421   -1.0252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3295   -1.4284   -0.8620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5150   -1.4602    0.9054 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5284   -0.3497   -1.8820 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8466    0.5498   -1.6356 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7088    1.1156    0.5775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0010   -0.0924    2.3067 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  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10  5  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
 10 17  1  0
M  END
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3D SDF for HMDB0001538 (3-Pyridylacetic acid)

  Mrv1652305261923582D          

 10 10  0  0  0  0            999 V2000
   11.5275   -5.8963    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5275   -6.7250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.2462   -5.4910    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.8342   -5.4812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1133   -5.8823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4055   -5.4584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1002   -6.7072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6846   -5.8596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3793   -7.1083    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.6715   -6.6845    0.0000 C   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
  4  1  1  0  0  0  0
  6  5  1  0  0  0  0
  7  5  2  0  0  0  0
  8  6  2  0  0  0  0
  9  7  1  0  0  0  0
 10  8  1  0  0  0  0
 10  9  2  0  0  0  0
  4  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001538

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)CC1=CN=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C7H7NO2/c9-7(10)4-6-2-1-3-8-5-6/h1-3,5H,4H2,(H,9,10)

> <INCHI_KEY>
WGNUNYPERJMVRM-UHFFFAOYSA-N

> <FORMULA>
C7H7NO2

> <MOLECULAR_WEIGHT>
137.136

> <EXACT_MASS>
137.047678473

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
13.18475033573732

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(pyridin-3-yl)acetic acid

> <ALOGPS_LOGP>
0.43

> <JCHEM_LOGP>
-0.5933040532539456

> <ALOGPS_LOGS>
-0.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.613664076629797

> <JCHEM_PKA_STRONGEST_BASIC>
4.973937384361667

> <JCHEM_POLAR_SURFACE_AREA>
50.19

> <JCHEM_REFRACTIVITY>
35.2087

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.83e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-pyridylacetic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0001538 (3-Pyridylacetic acid)

HMDB0001538
     RDKit          3D
3-Pyridylacetic acid
 17 17  0  0  0  0  0  0  0  0999 V2000
   -1.8230    1.4794   -0.1379 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2442    0.2945   -0.1227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5705   -0.0236   -0.2781 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2495   -0.8058    0.0734 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1215   -0.2736    0.2220 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9236   -0.0934   -0.8950 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2042    0.4042   -0.7528 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7016    0.7281    0.5014 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8942    0.5383    1.5485 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6482    0.0593    1.4566 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8443   -0.6421   -1.0252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3295   -1.4284   -0.8620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5150   -1.4602    0.9054 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5284   -0.3497   -1.8820 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8466    0.5498   -1.6356 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7088    1.1156    0.5775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0010   -0.0924    2.3067 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  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10  5  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
 10 17  1  0
M  END
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PDB for HMDB0001538 (3-Pyridylacetic acid)

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  C   UNK     0      21.518 -11.006   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      21.518 -12.553   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      22.860 -10.250   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      20.224 -10.232   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      18.878 -10.980   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      17.557 -10.189   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      18.854 -12.520   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      16.211 -10.938   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      17.508 -13.269   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      16.187 -12.478   0.000  0.00  0.00           C+0
CONECT    1    2    3    4                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    5                                                       
CONECT    5    6    7    4                                                  
CONECT    6    5    8                                                       
CONECT    7    5    9                                                       
CONECT    8    6   10                                                       
CONECT    9    7   10                                                       
CONECT   10    8    9                                                       
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for HMDB0001538 (3-Pyridylacetic acid)

COMPND    HMDB0001538
HETATM    1  O1  UNL     1      -1.823   1.479  -0.138  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.244   0.294  -0.123  1.00  0.00           C  
HETATM    3  O2  UNL     1      -3.571  -0.024  -0.278  1.00  0.00           O  
HETATM    4  C2  UNL     1      -1.249  -0.806   0.073  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.121  -0.274   0.222  1.00  0.00           C  
HETATM    6  C4  UNL     1       0.924  -0.093  -0.895  1.00  0.00           C  
HETATM    7  C5  UNL     1       2.204   0.404  -0.753  1.00  0.00           C  
HETATM    8  C6  UNL     1       2.702   0.728   0.501  1.00  0.00           C  
HETATM    9  N1  UNL     1       1.894   0.538   1.549  1.00  0.00           N  
HETATM   10  C7  UNL     1       0.648   0.059   1.457  1.00  0.00           C  
HETATM   11  H1  UNL     1      -3.844  -0.642  -1.025  1.00  0.00           H  
HETATM   12  H2  UNL     1      -1.330  -1.428  -0.862  1.00  0.00           H  
HETATM   13  H3  UNL     1      -1.515  -1.460   0.905  1.00  0.00           H  
HETATM   14  H4  UNL     1       0.528  -0.350  -1.882  1.00  0.00           H  
HETATM   15  H5  UNL     1       2.847   0.550  -1.636  1.00  0.00           H  
HETATM   16  H6  UNL     1       3.709   1.116   0.577  1.00  0.00           H  
HETATM   17  H7  UNL     1      -0.001  -0.092   2.307  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   11
CONECT    4    5   12   13
CONECT    5    6    6   10
CONECT    6    7   14
CONECT    7    8    8   15
CONECT    8    9   16
CONECT    9   10   10
CONECT   10   17
END
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SMILES for HMDB0001538 (3-Pyridylacetic acid)

OC(=O)CC1=CN=CC=C1
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INCHI for HMDB0001538 (3-Pyridylacetic acid)

InChI=1S/C7H7NO2/c9-7(10)4-6-2-1-3-8-5-6/h1-3,5H,4H2,(H,9,10)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC7H7NO2
Average Molecular Weight137.136
Monoisotopic Molecular Weight137.047678473
IUPAC Name2-(pyridin-3-yl)acetic acid
Traditional Name3-pyridylacetic acid
CAS Registry Number501-81-5
SMILES
OC(=O)CC1=CN=CC=C1
InChI Identifier
InChI=1S/C7H7NO2/c9-7(10)4-6-2-1-3-8-5-6/h1-3,5H,4H2,(H,9,10)
InChI KeyWGNUNYPERJMVRM-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyridines and derivatives. Pyridines and derivatives are compounds containing a pyridine ring, which is a six-member aromatic heterocycle which consists of one nitrogen atom and five carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassNot Available
Direct ParentPyridines and derivatives
Alternative Parents
Substituents
  • Pyridine
  • Heteroaromatic compound
  • Azacycle
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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 Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified2.47 +/- 1.55 uMAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022679
KNApSAcK IDNot Available
Chemspider ID106
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID6308
PubChem Compound108
PDB IDNot Available
ChEBI ID86390
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis Referenceaquet, Andre; Marison, Ian W.; Meyer, Hans Peter; Von Stockar, Urs. Choice of a method for in situ recovery of 3-pyridylacetic acid formed by biotransformation with Pseudomonas oleovorans. Chimia (1996), 50(9), 426-427.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Zwickenpflug W, Tyroller S, Richter E: Metabolism of myosmine in Wistar rats. Drug Metab Dispos. 2005 Nov;33(11):1648-56. Epub 2005 Aug 3. [PubMed:16079272 ]
  2. GINOULHIAC E, TENCONI LT, CHIANCONE FM: 3-Pyridineacetic acid and nicotinic acid: blood levels, urinary elimination and excretion of nicotinic acid derivatives in man. Nature. 1962 Mar 10;193:948-9. [PubMed:13898750 ]