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Showing metabocard for N-Methylpyridinium (HMDB0240545)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2019-10-11 16:10:34 UTC
Update Date2022-03-07 03:18:18 UTC
HMDB IDHMDB0240545
Secondary Accession NumbersNone
Metabolite Identification
Common NameN-Methylpyridinium
DescriptionN-Methylpyridinium belongs to the class of organic compounds known as n-methylpyridinium compounds. These are methylpyridines that carry a methyl group at the 1-position. Based on a literature review a significant number of articles have been published on N-Methylpyridinium.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0240545 (N-Methylpyridinium)


  Mrv1652310111918102D          

  7  7  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  2  0  0  0  0
  7  1  1  0  0  0  0
  7  5  2  0  0  0  0
  7  6  1  0  0  0  0
M  CHG  1   7   1
M  END
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3D MOL for HMDB0240545 (N-Methylpyridinium)

HMDB0240545
     RDKit          3D
N-Methylpyridinium
 15 15  0  0  0  0  0  0  0  0999 V2000
   -2.1723    0.0832   -0.1682 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7204    0.0184   -0.0595 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.0596   -1.1451    0.0369 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3152   -1.2051    0.1398 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0813   -0.0602    0.1485 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4001    1.1366    0.0492 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0169    1.1438   -0.0522 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6094    0.6349    0.7024 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4931    0.5659   -1.1171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5459   -0.9556   -0.0813 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6884   -2.0476    0.0283 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8161   -2.1685    0.2163 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1585   -0.1256    0.2299 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9967    2.0408    0.0554 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4958    2.0841   -0.1285 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
  7 15  1  0
M  CHG  1   2   1
M  END
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3D SDF for HMDB0240545 (N-Methylpyridinium)


  Mrv1652310111918102D          

  7  7  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  2  0  0  0  0
  7  1  1  0  0  0  0
  7  5  2  0  0  0  0
  7  6  1  0  0  0  0
M  CHG  1   7   1
M  END
> <DATABASE_ID>
HMDB0240545

> <DATABASE_NAME>
hmdb

> <SMILES>
C[N+]1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C6H8N/c1-7-5-3-2-4-6-7/h2-6H,1H3/q+1

> <INCHI_KEY>
PQBAWAQIRZIWIV-UHFFFAOYSA-N

> <FORMULA>
C6H8N

> <MOLECULAR_WEIGHT>
94.136

> <EXACT_MASS>
94.065125682

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
10.735441955631517

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-methylpyridin-1-ium

> <ALOGPS_LOGP>
-3.66

> <JCHEM_LOGP>
-3.1877949708050792

> <ALOGPS_LOGS>
-2.98

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_POLAR_SURFACE_AREA>
3.88

> <JCHEM_REFRACTIVITY>
30.0565

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.37e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-methylpyridinium

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0240545 (N-Methylpyridinium)

HMDB0240545
     RDKit          3D
N-Methylpyridinium
 15 15  0  0  0  0  0  0  0  0999 V2000
   -2.1723    0.0832   -0.1682 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7204    0.0184   -0.0595 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.0596   -1.1451    0.0369 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3152   -1.2051    0.1398 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0813   -0.0602    0.1485 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4001    1.1366    0.0492 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0169    1.1438   -0.0522 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6094    0.6349    0.7024 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4931    0.5659   -1.1171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5459   -0.9556   -0.0813 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6884   -2.0476    0.0283 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8161   -2.1685    0.2163 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1585   -0.1256    0.2299 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9967    2.0408    0.0554 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4958    2.0841   -0.1285 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
  7 15  1  0
M  CHG  1   2   1
M  END
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PDB for HMDB0240545 (N-Methylpyridinium)

HEADER    PROTEIN                                 11-OCT-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-OCT-19         0                                  
HETATM    1  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+1
CONECT    1    7                                                            
CONECT    2    3    4                                                       
CONECT    3    2    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    7                                                       
CONECT    6    4    7                                                       
CONECT    7    1    5    6                                                  
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0240545 (N-Methylpyridinium)

COMPND    HMDB0240545
HETATM    1  C1  UNL     1      -2.172   0.083  -0.168  1.00  0.00           C  
HETATM    2  N1  UNL     1      -0.720   0.018  -0.059  1.00  0.00           N1+
HETATM    3  C2  UNL     1      -0.060  -1.145   0.037  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.315  -1.205   0.140  1.00  0.00           C  
HETATM    5  C4  UNL     1       2.081  -0.060   0.148  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.400   1.137   0.049  1.00  0.00           C  
HETATM    7  C6  UNL     1       0.017   1.144  -0.052  1.00  0.00           C  
HETATM    8  H1  UNL     1      -2.609   0.635   0.702  1.00  0.00           H  
HETATM    9  H2  UNL     1      -2.493   0.566  -1.117  1.00  0.00           H  
HETATM   10  H3  UNL     1      -2.546  -0.956  -0.081  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.688  -2.048   0.028  1.00  0.00           H  
HETATM   12  H5  UNL     1       1.816  -2.168   0.216  1.00  0.00           H  
HETATM   13  H6  UNL     1       3.158  -0.126   0.230  1.00  0.00           H  
HETATM   14  H7  UNL     1       1.997   2.041   0.055  1.00  0.00           H  
HETATM   15  H8  UNL     1      -0.496   2.084  -0.128  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
CONECT    7   15
END
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SMILES for HMDB0240545 (N-Methylpyridinium)

C[N+]1=CC=CC=C1
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INCHI for HMDB0240545 (N-Methylpyridinium)

InChI=1S/C6H8N/c1-7-5-3-2-4-6-7/h2-6H,1H3/q+1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1-MethylpyridiniumChEBI
1-Methylpyridinium iodideHMDB
1-Methylpyridinium dibromoiodate (1-)HMDB
1-Methylpyridinium chlorideHMDB
1-Methylpyridinium mu-iodotetraiododimercurate (1-)HMDB
Chemical FormulaC6H8N
Average Molecular Weight94.136
Monoisotopic Molecular Weight94.065125682
IUPAC Name1-methylpyridin-1-ium
Traditional NameN-methylpyridinium
CAS Registry NumberNot Available
SMILES
C[N+]1=CC=CC=C1
InChI Identifier
InChI=1S/C6H8N/c1-7-5-3-2-4-6-7/h2-6H,1H3/q+1
InChI KeyPQBAWAQIRZIWIV-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as n-methylpyridinium compounds. These are methylpyridines that carry a methyl group at the 1-position.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassMethylpyridines
Direct ParentN-methylpyridinium compounds
Alternative Parents
Substituents
  • N-methylpyridinium
  • Pyridinium
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Organic cation
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
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
PropertyValueSource
logP-3.7ALOGPS
logP-3.2ChemAxon
logS-3ALOGPS
Physiological Charge1ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area3.88 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity30.06 m³·mol⁻¹ChemAxon
Polarizability10.74 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
DeepCCS[M+H]+116.26930932474
DeepCCS[M-H]-113.48930932474
DeepCCS[M-2H]-149.90730932474
DeepCCS[M+Na]+124.81330932474
AllCCS[M+H]+113.932859911
AllCCS[M+H-H2O]+108.732859911
AllCCS[M+NH4]+118.832859911
AllCCS[M+Na]+120.232859911
AllCCS[M-H]-121.632859911
AllCCS[M+Na-2H]-124.632859911
AllCCS[M+HCOO]-128.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
N-MethylpyridiniumC[N+]1=CC=CC=C11124.5Standard polar33892256
N-MethylpyridiniumC[N+]1=CC=CC=C1830.8Standard non polar33892256
N-MethylpyridiniumC[N+]1=CC=CC=C1796.2Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - N-Methylpyridinium GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Methylpyridinium GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Methylpyridinium 10V, Positive-QTOFsplash10-0006-9000000000-5589b8222789427c2a352019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Methylpyridinium 20V, Positive-QTOFsplash10-0006-9000000000-f49f9c7ed7757bce52192019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Methylpyridinium 40V, Positive-QTOFsplash10-014i-9000000000-5491e35cf5c1fa44211c2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Methylpyridinium 10V, Positive-QTOFsplash10-0006-9000000000-6084bf34f359c4b44fa92021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Methylpyridinium 20V, Positive-QTOFsplash10-00kf-9000000000-ddd48e9d68a7ccfbd3d02021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Methylpyridinium 40V, Positive-QTOFsplash10-014i-9000000000-5a9f51ae8c7fc25902df2021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB093740
KNApSAcK IDNot Available
Chemspider ID13008
KEGG Compound IDC02724
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkMethylpyridinium
METLIN IDNot Available
PubChem Compound13597
PDB IDNot Available
ChEBI ID15761
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 ReferencesNot Available