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Showing metabocard for 2-Methylpyridine (HMDB0061888)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2014-10-08 15:56:39 UTC
Update Date2023-02-21 17:30:33 UTC
HMDB IDHMDB0061888
Secondary Accession Numbers
  • HMDB61888
Metabolite Identification
Common Name2-Methylpyridine
Description2-Methylpyridine, also known as alpha-picoline or 2-mepy, belongs to the class of organic compounds known as methylpyridines. These are organic compounds containing a pyridine ring substituted at one or more positions by a methyl group. 2-Methylpyridine, or 2-picoline, is the compound described with formula C6H7N. 2-Methylpyridine is a colorless liquid that has an unpleasant odor similar to pyridine. 2-Methylpyridine is a very strong basic compound (based on its pKa). 2-Methylpyridine is a bitter and sweat tasting compound. Outside of the human body, 2-Methylpyridine has been detected, but not quantified in, corns and tea. This could make 2-methylpyridine a potential biomarker for the consumption of these foods. Pyridines including 2-Methylpyridine are most crudely prepared by the reaction of acetylene and hydrogen cyanide.
Structure
Data?1677000633
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0061888 (2-Methylpyridine)

  Mrv1652304272018112D          

  7  7  0  0  0  0            999 V2000
   -0.8250    1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  2  0  0  0  0
  5  7  2  0  0  0  0
  6  7  1  0  0  0  0
M  END
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3D MOL for HMDB0061888 (2-Methylpyridine)

HMDB0061888
     RDKit          3D
2-Methylpyridine
 14 14  0  0  0  0  0  0  0  0999 V2000
    2.2468   -0.0370   -0.0617 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7613    0.1097   -0.0286 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0477   -1.0017    0.0376 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4301   -0.9171    0.0705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0290    0.3254    0.0360 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1950    1.4316   -0.0307 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1489    1.3093   -0.0610 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5905   -0.4520   -1.0430 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5964   -0.7824    0.7074 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7542    0.9033    0.1859 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4482   -1.9748    0.0640 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0580   -1.7988    0.1227 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1025    0.4746    0.0582 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6842    2.4100   -0.0574 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  4 12  1  0
  5 13  1  0
  6 14  1  0
M  END
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3D SDF for HMDB0061888 (2-Methylpyridine)

  Mrv1652304272018112D          

  7  7  0  0  0  0            999 V2000
   -0.8250    1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  2  0  0  0  0
  5  7  2  0  0  0  0
  6  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0061888

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CC=CC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C6H7N/c1-6-4-2-3-5-7-6/h2-5H,1H3

> <INCHI_KEY>
BSKHPKMHTQYZBB-UHFFFAOYSA-N

> <FORMULA>
C6H7N

> <MOLECULAR_WEIGHT>
93.1265

> <EXACT_MASS>
93.057849229

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
10.384814328327693

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-methylpyridine

> <ALOGPS_LOGP>
1.25

> <JCHEM_LOGP>
0.8869435579999998

> <ALOGPS_LOGS>
0.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
5.8116853236678585

> <JCHEM_POLAR_SURFACE_AREA>
12.89

> <JCHEM_REFRACTIVITY>
28.492599999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.02e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
α-methylpyridine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0061888 (2-Methylpyridine)

HMDB0061888
     RDKit          3D
2-Methylpyridine
 14 14  0  0  0  0  0  0  0  0999 V2000
    2.2468   -0.0370   -0.0617 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7613    0.1097   -0.0286 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0477   -1.0017    0.0376 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4301   -0.9171    0.0705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0290    0.3254    0.0360 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1950    1.4316   -0.0307 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1489    1.3093   -0.0610 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5905   -0.4520   -1.0430 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5964   -0.7824    0.7074 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7542    0.9033    0.1859 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4482   -1.9748    0.0640 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0580   -1.7988    0.1227 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1025    0.4746    0.0582 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6842    2.4100   -0.0574 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  4 12  1  0
  5 13  1  0
  6 14  1  0
M  END
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PDB for HMDB0061888 (2-Methylpyridine)

HEADER    PROTEIN                                 27-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-APR-20         0                                  
HETATM    1  C   UNK     0      -1.540   2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.770   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -1.540   0.000   0.000  0.00  0.00           N+0
CONECT    1    6                                                            
CONECT    2    3    4                                                       
CONECT    3    2    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    7                                                       
CONECT    6    1    4    7                                                  
CONECT    7    5    6                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0061888 (2-Methylpyridine)

COMPND    HMDB0061888
HETATM    1  C1  UNL     1       2.247  -0.037  -0.062  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.761   0.110  -0.029  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.048  -1.002   0.038  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.430  -0.917   0.071  1.00  0.00           C  
HETATM    5  C5  UNL     1      -2.029   0.325   0.036  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.195   1.432  -0.031  1.00  0.00           C  
HETATM    7  N1  UNL     1       0.149   1.309  -0.061  1.00  0.00           N  
HETATM    8  H1  UNL     1       2.591  -0.452  -1.043  1.00  0.00           H  
HETATM    9  H2  UNL     1       2.596  -0.782   0.707  1.00  0.00           H  
HETATM   10  H3  UNL     1       2.754   0.903   0.186  1.00  0.00           H  
HETATM   11  H4  UNL     1       0.448  -1.975   0.064  1.00  0.00           H  
HETATM   12  H5  UNL     1      -2.058  -1.799   0.123  1.00  0.00           H  
HETATM   13  H6  UNL     1      -3.103   0.475   0.058  1.00  0.00           H  
HETATM   14  H7  UNL     1      -1.684   2.410  -0.057  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    3    7
CONECT    3    4   11
CONECT    4    5    5   12
CONECT    5    6   13
CONECT    6    7    7   14
END
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SMILES for HMDB0061888 (2-Methylpyridine)

CC1=CC=CC=N1
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INCHI for HMDB0061888 (2-Methylpyridine)

InChI=1S/C6H7N/c1-6-4-2-3-5-7-6/h2-5H,1H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-MepyChEBI
2-PicolineChEBI
alpha-PicolineChEBI
O-MethylpyridineChEBI
O-PicolineChEBI
a-PicolineGenerator
Α-picolineGenerator
2-Picolinium bromideMeSH
Chemical FormulaC6H7N
Average Molecular Weight93.1265
Monoisotopic Molecular Weight93.057849229
IUPAC Name2-methylpyridine
Traditional Nameα-methylpyridine
CAS Registry Number109-06-8
SMILES
CC1=CC=CC=N1
InChI Identifier
InChI=1S/C6H7N/c1-6-4-2-3-5-7-6/h2-5H,1H3
InChI KeyBSKHPKMHTQYZBB-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as methylpyridines. These are organic compounds containing a pyridine ring substituted at one or more positions by a methyl group.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassMethylpyridines
Direct ParentMethylpyridines
Alternative Parents
Substituents
  • Methylpyridine
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
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
  • Saliva
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Not SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB004399
KNApSAcK IDNot Available
Chemspider ID13839199
KEGG Compound IDC14447
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link2-methylpyridine
METLIN IDNot Available
PubChem Compound7975
PDB IDNot Available
ChEBI ID50415
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Haviv F, DeNet RW, Michaels RJ, Ratajczyk JD, Carter GW, Young PR: 2-[(Phenylthio)methyl]pyridine derivatives: new antiinflammatory agents. J Med Chem. 1983 Feb;26(2):218-22. [PubMed:6827539 ]
  2. Wikipedia [Link]
  3. Robert Osborne, Kevin D. Bailey, 'Preparation of 2-chloro-5-methylpyridine.' U.S. Patent US4612377, issued September, 1984. [Link]
  4. Dev D. Suresh, Robert DiCosimo, Richard Loiseau, Maria S. Friedrich, Hsiao-Chiung Szabo, 'Preparation of 3-methylpyridine from 2-methylglutaronitrile.' U.S. Patent US5066809, issued June, 1985. [Link]