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Showing NP-Card for 3-Pyridylacetic acid (NP0000061)

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Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-08-15 04:56:50 UTC
NP-MRD IDNP0000061
Secondary Accession NumbersNone
Natural Product 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 NP0000061 (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
Download

3D MOL for NP0000061 (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
Download

3D SDF for NP0000061 (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>
NP0000061

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
Download

3D-SDF for NP0000061 (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 NP0000061 (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 NP0000061 (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 NP0000061 (3-Pyridylacetic acid)

OC(=O)CC1=CN=CC=C1
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INCHI for NP0000061 (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 JSmol
Synonyms
ValueSource
3-PyridylacetateGenerator
2-(3-Pyridyl)acetateHMDB
2-(3-Pyridyl)acetic acidHMDB
2-(Pyridin-3-yl)acetateHMDB
2-(Pyridin-3-yl)acetic acidHMDB
3-CarboxymethylpyridineHMDB
a-(3-Pyridyl)acetateHMDB
a-(3-Pyridyl)acetic acidHMDB
alpha-(3-Pyridyl)acetateHMDB
alpha-(3-Pyridyl)acetic acidHMDB
ColetinHMDB
LessterolHMDB
LioxoneHMDB
MinedilHMDB
PiridilHMDB
PiristerolHMDB
Pyridin-3-ylacetateHMDB
Pyridin-3-ylacetic acidHMDB
ToneonHMDB
2-(3-Pyridine)acetic acidHMDB
3-Pyridineacetic acidHMDB
Chemical FormulaC7H7NO2
Average Mass137.1360 Da
Monoisotopic Mass137.04768 Da
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, simulated)V.dorna832021-08-23View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)V.dorna832021-08-23View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, simulated)V.dorna832021-07-21View Spectrum
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
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
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point144 °Chttps://pubchem.ncbi.nlm.nih.gov/compound/3-Pyridineacetic-acid#section=Melting-Point
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility58.3 g/LALOGPS
logP0.43ALOGPS
logP-0.59ChemAxon
logS-0.37ALOGPS
pKa (Strongest Acidic)3.61ChemAxon
pKa (Strongest Basic)4.97ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area50.19 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity35.21 m³·mol⁻¹ChemAxon
Polarizability13.18 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001538
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB 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
Good Scents IDNot Available
References
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 ]
  3. Ganna A, Salihovic S, Sundstrom J, Broeckling CD, Hedman AK, Magnusson PK, Pedersen NL, Larsson A, Siegbahn A, Zilmer M, Prenni J, Arnlov J, Lind L, Fall T, Ingelsson E: Large-scale metabolomic profiling identifies novel biomarkers for incident coronary heart disease. PLoS Genet. 2014 Dec 11;10(12):e1004801. doi: 10.1371/journal.pgen.1004801. eCollection 2014 Dec. [PubMed:25502724 ]
  4. Miyamoto Y, Banno Y, Yamashita T, Fujimoto T, Oi S, Moritoh Y, Asakawa T, Kataoka O, Yashiro H, Takeuchi K, Suzuki N, Ikedo K, Kosaka T, Tsubotani S, Tani A, Sasaki M, Funami M, Amano M, Yamamoto Y, Aertgeerts K, Yano J, Maezaki H: Discovery of a 3-pyridylacetic acid derivative (TAK-100) as a potent, selective and orally active dipeptidyl peptidase IV (DPP-4) inhibitor. J Med Chem. 2011 Feb 10;54(3):831-50. doi: 10.1021/jm101236h. Epub 2011 Jan 10. [PubMed:21218817 ]
  5. Liao X, Zhu J, Rubab M, Feng YL, Poon R: An analytical method for the measurement of acid metabolites of tryptophan-NAD pathway and related acids in urine. J Chromatogr B Analyt Technol Biomed Life Sci. 2010 Apr 15;878(13-14):1003-6. doi: 10.1016/j.jchromb.2010.02.017. Epub 2010 Feb 23. [PubMed:20299289 ]