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Showing metabocard for 4-Methylpyridine (HMDB0302405)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 17:32:07 UTC
Update Date2021-09-23 17:32:08 UTC
HMDB IDHMDB0302405
Secondary Accession NumbersNone
Metabolite Identification
Common Name4-Methylpyridine
Description4-methylpyridine, also known as 4-mepy or 4-picoline, is a member of the class of compounds known as methylpyridines. Methylpyridines are organic compounds containing a pyridine ring substituted at one or more positions by a methyl group. 4-methylpyridine is soluble (in water) and a very strong basic compound (based on its pKa). 4-methylpyridine can be found in fig and tea, which makes 4-methylpyridine a potential biomarker for the consumption of these food products. 4-methylpyridine is the organic compound with the formula CH3C5H4N. It is one of the three isomers of methylpyridine. This pungent Liquid is a building block for the synthesis of other heterocyclic compounds. Its conjugate acid, the 4-methylpyridinium ion, has a pKa of 5.98, about 0.7 units above that of pyridine itself .
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0302405 (4-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  4  2  0  0  0  0
  2  6  1  0  0  0  0
  3  5  1  0  0  0  0
  3  6  2  0  0  0  0
  4  7  1  0  0  0  0
  5  7  2  0  0  0  0
M  END
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3D MOL for HMDB0302405 (4-Methylpyridine)

HMDB0302405
     RDKit          3D
4-Methylpyridine
 14 14  0  0  0  0  0  0  0  0999 V2000
   -1.9290   -0.4094   -0.0260 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4465   -0.1315   -0.0090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0449    1.1730    0.0090 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3032    1.4799    0.0251 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2034    0.4808    0.0226 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8055   -0.8146    0.0047 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4685   -1.1423   -0.0115 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1228   -1.3668   -0.5161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4170    0.4359   -0.5718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2613   -0.4170    1.0465 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8107    1.9628    0.0105 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5667    2.5283    0.0391 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5387   -1.6147    0.0028 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1462   -2.1645   -0.0257 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
  6 13  1  0
  7 14  1  0
M  END
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3D SDF for HMDB0302405 (4-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  4  2  0  0  0  0
  2  6  1  0  0  0  0
  3  5  1  0  0  0  0
  3  6  2  0  0  0  0
  4  7  1  0  0  0  0
  5  7  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0302405

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CC=NC=C1

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

> <INCHI_KEY>
FKNQCJSGGFJEIZ-UHFFFAOYSA-N

> <FORMULA>
C6H7N

> <MOLECULAR_WEIGHT>
93.1265

> <EXACT_MASS>
93.057849229

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
10.303953264770996

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-methylpyridine

> <ALOGPS_LOGP>
1.14

> <JCHEM_LOGP>
1.2689947783333335

> <ALOGPS_LOGS>
0.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
5.849412521114263

> <JCHEM_POLAR_SURFACE_AREA>
12.89

> <JCHEM_REFRACTIVITY>
28.9423

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.95e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-methylpyridine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0302405 (4-Methylpyridine)

HMDB0302405
     RDKit          3D
4-Methylpyridine
 14 14  0  0  0  0  0  0  0  0999 V2000
   -1.9290   -0.4094   -0.0260 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4465   -0.1315   -0.0090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0449    1.1730    0.0090 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3032    1.4799    0.0251 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2034    0.4808    0.0226 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8055   -0.8146    0.0047 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4685   -1.1423   -0.0115 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1228   -1.3668   -0.5161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4170    0.4359   -0.5718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2613   -0.4170    1.0465 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8107    1.9628    0.0105 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5667    2.5283    0.0391 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5387   -1.6147    0.0028 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1462   -2.1645   -0.0257 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
  6 13  1  0
  7 14  1  0
M  END
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PDB for HMDB0302405 (4-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    4    6                                                       
CONECT    3    5    6                                                       
CONECT    4    2    7                                                       
CONECT    5    3    7                                                       
CONECT    6    1    2    3                                                  
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 HMDB0302405 (4-Methylpyridine)

COMPND    HMDB0302405
HETATM    1  C1  UNL     1      -1.929  -0.409  -0.026  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.447  -0.131  -0.009  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.045   1.173   0.009  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.303   1.480   0.025  1.00  0.00           C  
HETATM    5  N1  UNL     1       2.203   0.481   0.023  1.00  0.00           N  
HETATM    6  C5  UNL     1       1.806  -0.815   0.005  1.00  0.00           C  
HETATM    7  C6  UNL     1       0.468  -1.142  -0.012  1.00  0.00           C  
HETATM    8  H1  UNL     1      -2.123  -1.367  -0.516  1.00  0.00           H  
HETATM    9  H2  UNL     1      -2.417   0.436  -0.572  1.00  0.00           H  
HETATM   10  H3  UNL     1      -2.261  -0.417   1.047  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.811   1.963   0.010  1.00  0.00           H  
HETATM   12  H5  UNL     1       1.567   2.528   0.039  1.00  0.00           H  
HETATM   13  H6  UNL     1       2.539  -1.615   0.003  1.00  0.00           H  
HETATM   14  H7  UNL     1       0.146  -2.165  -0.026  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
CONECT    6    7    7   13
CONECT    7   14
END
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SMILES for HMDB0302405 (4-Methylpyridine)

CC1=CC=NC=C1
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INCHI for HMDB0302405 (4-Methylpyridine)

InChI=1S/C6H7N/c1-6-2-4-7-5-3-6/h2-5H,1H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
4-MepyChEBI
4-PicolineChEBI
gamma-PicolineChEBI
p-MethylpyridineChEBI
p-PicolineChEBI
g-PicolineGenerator
Γ-picolineGenerator
4-MethylpyridiniumMeSH
Chemical FormulaC6H7N
Average Molecular Weight93.1265
Monoisotopic Molecular Weight93.057849229
IUPAC Name4-methylpyridine
Traditional Name4-methylpyridine
CAS Registry NumberNot Available
SMILES
CC1=CC=NC=C1
InChI Identifier
InChI=1S/C6H7N/c1-6-2-4-7-5-3-6/h2-5H,1H3
InChI KeyFKNQCJSGGFJEIZ-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
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateLiquid
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 IDFDB004424
KNApSAcK IDC00054275
Chemspider ID13874733
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link4-Methylpyridine
METLIN IDNot Available
PubChem Compound7963
PDB IDNot Available
ChEBI ID32547
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1206761
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available