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Showing metabocard for 3-Methylpyridine (HMDB0061887)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2014-10-08 15:56:38 UTC
Update Date2023-02-21 17:30:33 UTC
HMDB IDHMDB0061887
Secondary Accession Numbers
  • HMDB61887
Metabolite Identification
Common Name3-Methylpyridine
Description3-Methylpyridine, also known as beta-picoline or 3-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. 3-Methylpyridine is a very strong basic compound (based on its pKa). A methylpyridine that is pyridine substituted by a methyl group at position 3. Outside of the human body, 3-Methylpyridine has been detected, but not quantified in, sweet oranges and tea. This could make 3-methylpyridine a potential biomarker for the consumption of these foods.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0061887 (3-Methylpyridine)

  Mrv1652304272018142D          

  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   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7145    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   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    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  6  1  0  0  0  0
  4  7  2  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
M  END
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3D MOL for HMDB0061887 (3-Methylpyridine)

HMDB0061887
     RDKit          3D
3-Methylpyridine
 14 14  0  0  0  0  0  0  0  0999 V2000
   -2.0289    0.4087   -0.1837 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5906    0.0144   -0.0604 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3848    0.9748    0.0978 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7138    0.5822    0.2101 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0974   -0.7435    0.1689 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1046   -1.6398    0.0128 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1865   -1.3040   -0.0990 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6762   -0.4838    0.0098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2432    0.7551   -1.2189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2815    1.2082    0.5697 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0654    2.0007    0.1274 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4744    1.3440    0.3342 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1385   -1.0522    0.2567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9721   -2.0649   -0.2256 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
  7 14  1  0
M  END
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3D SDF for HMDB0061887 (3-Methylpyridine)

  Mrv1652304272018142D          

  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   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7145    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   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    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  6  1  0  0  0  0
  4  7  2  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0061887

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CN=CC=C1

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

> <INCHI_KEY>
ITQTTZVARXURQS-UHFFFAOYSA-N

> <FORMULA>
C6H7N

> <MOLECULAR_WEIGHT>
93.1265

> <EXACT_MASS>
93.057849229

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
10.31154883866584

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-methylpyridine

> <ALOGPS_LOGP>
1.11

> <JCHEM_LOGP>
1.2689947783333335

> <ALOGPS_LOGS>
0.33

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
5.627866775155743

> <JCHEM_POLAR_SURFACE_AREA>
12.89

> <JCHEM_REFRACTIVITY>
28.942299999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.97e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-methylpyridine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0061887 (3-Methylpyridine)

HMDB0061887
     RDKit          3D
3-Methylpyridine
 14 14  0  0  0  0  0  0  0  0999 V2000
   -2.0289    0.4087   -0.1837 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5906    0.0144   -0.0604 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3848    0.9748    0.0978 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7138    0.5822    0.2101 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0974   -0.7435    0.1689 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1046   -1.6398    0.0128 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1865   -1.3040   -0.0990 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6762   -0.4838    0.0098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2432    0.7551   -1.2189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2815    1.2082    0.5697 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0654    2.0007    0.1274 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4744    1.3440    0.3342 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1385   -1.0522    0.2567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9721   -2.0649   -0.2256 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
  7 14  1  0
M  END
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PDB for HMDB0061887 (3-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      -1.540   0.000   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      -0.770   1.334   0.000  0.00  0.00           N+0
CONECT    1    6                                                            
CONECT    2    3    4                                                       
CONECT    3    2    6                                                       
CONECT    4    2    7                                                       
CONECT    5    6    7                                                       
CONECT    6    1    3    5                                                  
CONECT    7    4    5                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0061887 (3-Methylpyridine)

COMPND    HMDB0061887
HETATM    1  C1  UNL     1      -2.029   0.409  -0.184  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.591   0.014  -0.060  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.385   0.975   0.098  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.714   0.582   0.210  1.00  0.00           C  
HETATM    5  C5  UNL     1       2.097  -0.743   0.169  1.00  0.00           C  
HETATM    6  N1  UNL     1       1.105  -1.640   0.013  1.00  0.00           N  
HETATM    7  C6  UNL     1      -0.187  -1.304  -0.099  1.00  0.00           C  
HETATM    8  H1  UNL     1      -2.676  -0.484   0.010  1.00  0.00           H  
HETATM    9  H2  UNL     1      -2.243   0.755  -1.219  1.00  0.00           H  
HETATM   10  H3  UNL     1      -2.282   1.208   0.570  1.00  0.00           H  
HETATM   11  H4  UNL     1       0.065   2.001   0.127  1.00  0.00           H  
HETATM   12  H5  UNL     1       2.474   1.344   0.334  1.00  0.00           H  
HETATM   13  H6  UNL     1       3.139  -1.052   0.257  1.00  0.00           H  
HETATM   14  H7  UNL     1      -0.972  -2.065  -0.226  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
CONECT    7   14
END
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SMILES for HMDB0061887 (3-Methylpyridine)

CC1=CN=CC=C1
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INCHI for HMDB0061887 (3-Methylpyridine)

InChI=1S/C6H7N/c1-6-3-2-4-7-5-6/h2-5H,1H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
3-MepyChEBI
3-PicolineChEBI
beta-PicolineChEBI
m-MethylpyridineChEBI
m-PicolineChEBI
b-PicolineGenerator
Β-picolineGenerator
Chemical FormulaC6H7N
Average Molecular Weight93.1265
Monoisotopic Molecular Weight93.057849229
IUPAC Name3-methylpyridine
Traditional Name3-methylpyridine
CAS Registry Number108-99-6
SMILES
CC1=CN=CC=C1
InChI Identifier
InChI=1S/C6H7N/c1-6-3-2-4-7-5-6/h2-5H,1H3
InChI KeyITQTTZVARXURQS-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 effectNot Available
Disposition
Biological locationSource
ProcessNot Available
Role
Industrial application
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 IDDB01996
Phenol Explorer Compound IDNot Available
FooDB IDFDB004416
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link3-Methylpyridine
METLIN IDNot Available
PubChem Compound7970
PDB IDNot Available
ChEBI ID39922
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. Veena Kushwaha, Singh RP, Katyal M: Metal complexation with 2-hydroxy-6-methylpyridine-3-carboxylic acid. Talanta. 1973 Apr;20(4):431-2. [PubMed:18961302 ]
  2. Wikipedia [Link]
  3. Bernard Gupton, 'Process for making 3-amino-2-chloro-4-methylpyridine.' U.S. Patent US20020052507, issued May 02, 2002. [Link]
  4. Helmut Beschke, Hans Schaefer, Gerd Schreyer, Wilhelm Alfons Schuler, Wolfgang Weigert, 'Catalyst for the production of pyridine and 3-methylpyridine.' U.S. Patent US3960766, issued February, 1971. [Link]
  5. Helmut Beschke, Franz-Ludwig Dahm, Heinz Friedrich, Gerd Schreyer, 'Process for the recovery of pyridine and 3-methylpyridine.' U.S. Patent US4237299, issued October, 1979. [Link]
  6. 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]