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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
PropertyValueSource
logP1.14ALOGPS
logP1.27ChemAxon
logS0.32ALOGPS
pKa (Strongest Basic)5.85ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area12.89 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity28.94 m³·mol⁻¹ChemAxon
Polarizability10.3 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+114.89832859911
AllCCS[M+H-H2O]+109.63632859911
AllCCS[M+Na]+121.24232859911
AllCCS[M+NH4]+119.8232859911
AllCCS[M-H]-117.8632859911
AllCCS[M+Na-2H]-120.91932859911
AllCCS[M+HCOO]-124.30832859911
DeepCCS[M+H]+120.10630932474
DeepCCS[M-H]-117.72330932474
DeepCCS[M-2H]-153.78730932474
DeepCCS[M+Na]+128.5430932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20228.986 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.64 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid793.7 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid329.1 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid110.6 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid215.4 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid62.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid284.2 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid300.6 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)262.6 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid636.9 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid38.8 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid856.2 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid207.4 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid267.7 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate506.4 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA336.5 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water165.0 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - 4-Methylpyridine QqQ 14V, positive-QTOFsplash10-0006-9000000000-cf6d2b1f296868a41fb02020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 4-Methylpyridine QqQ 16V, positive-QTOFsplash10-0006-9000000000-f28b5acf237330db39cd2020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 4-Methylpyridine QqQ 20V, positive-QTOFsplash10-0006-9000000000-c377759a238292231de92020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 4-Methylpyridine Orbitrap 3V, positive-QTOFsplash10-0006-9000000000-5a45b3d162e01c64295f2020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 4-Methylpyridine Orbitrap 4V, positive-QTOFsplash10-0006-9000000000-73a8d82a235aa15b5cbb2020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 4-Methylpyridine Orbitrap 5V, positive-QTOFsplash10-0006-9000000000-116bd856759c69e363022020-07-22HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 4-Methylpyridine n/a 6V, positive-QTOFsplash10-004i-9000000000-3bf262f96423e85a17562020-07-22HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylpyridine 10V, Positive-QTOFsplash10-0006-9000000000-90c0f2706e4d91aa25982016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylpyridine 20V, Positive-QTOFsplash10-0006-9000000000-2803318666b1703a07c22016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylpyridine 40V, Positive-QTOFsplash10-0fr6-9000000000-93a6b6d38867054d253a2016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylpyridine 10V, Negative-QTOFsplash10-0006-9000000000-78c945aa8b292854c0e42016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylpyridine 20V, Negative-QTOFsplash10-0006-9000000000-b8d4f86ab1fdd2fb00512016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylpyridine 40V, Negative-QTOFsplash10-0006-9000000000-8a769e961f6c29cb459c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylpyridine 10V, Positive-QTOFsplash10-0006-9000000000-d2c754e54d63cb0d96d52021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylpyridine 20V, Positive-QTOFsplash10-00kf-9000000000-9f5aca8f2ce69a372ce12021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylpyridine 40V, Positive-QTOFsplash10-0v00-9000000000-9e4c76f82fdbbf010b1c2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylpyridine 10V, Negative-QTOFsplash10-0006-9000000000-eef4c1f804c025cbb9782021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylpyridine 20V, Negative-QTOFsplash10-0006-9000000000-eef4c1f804c025cbb9782021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylpyridine 40V, Negative-QTOFsplash10-0006-9000000000-f4ea495fc86cef6b3c172021-10-21Wishart LabView Spectrum
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