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Showing NP-Card for 2-Methyl-1H-imidazole (NP0045089)

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Record Information
Version1.0
Created at2022-03-10 18:57:46 UTC
Updated at2022-03-10 22:16:58 UTC
NP-MRD IDNP0045089
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-Methyl-1H-imidazole
Description2-Methylimidazole, belongs to the class of organic compounds known as imidazoles. Imidazoles are compounds containing an imidazole ring, which is an aromatic five-membered ring, that includes two nitrogen atoms at positions 1 and 3, and three carbon atoms. 2-MethylImidazole has the chemical formula CH3C3H2N2H and is a methylated derivative of Imidazole on which a methyl group has been added at position C-2. It is a white or colorless solid that is highly soluble in polar organic solvents and water. It is a precursor to a range of drugs and is a ligand in coordination chemistry. 2-Methylimidazole is prepared by condensation of glyoxal, ammonia, and acetaldehyde, through the Radziszewski reaction. 2-Methylimidazole is a sterically hindered imidazole that is used to simulate the coordination of histidine to heme complexes. It can be deprotonated to make imidazolate-based coordination polymers. 2-Methylimidazole is a precursor to several members of the nitroimidazole antibiotics that are used to combat anaerobic bacterial and parasitic infections. 2-Methylimidazole has been found in the volatile fraction of Cannabis sativa (PMID: 26657499 ) And is likely a component of marijuana smoke (https://Doi.Org/10.1007/978-1-59259-947-9_2).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0045089 (2-Methyl-1H-imidazole)


  Mrv1652303202019002D          

  6  6  0  0  0  0            999 V2000
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  4  2  0  0  0  0
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
M  END
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3D MOL for NP0045089 (2-Methyl-1H-imidazole)

     RDKit          3D

 12 12  0  0  0  0  0  0  0  0999 V2000
    1.9414   -0.1494   -0.0381 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4357   -0.1786   -0.0117 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3472   -1.2736   -0.0052 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6424   -0.8985    0.0203 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6865    0.4850    0.0304 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3996    0.8753    0.0102 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2503    0.8675    0.2600 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3284   -0.3267   -1.0496 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2837   -0.8811    0.6905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5244   -1.5201    0.0318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5611    1.1298    0.0503 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0782    1.8702    0.0112 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  2  1  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  4 10  1  0
  5 11  1  0
  6 12  1  0
M  END
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3D SDF for NP0045089 (2-Methyl-1H-imidazole)


  Mrv1652303202019002D          

  6  6  0  0  0  0            999 V2000
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  4  2  0  0  0  0
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0045089

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=NC=CN1

> <INCHI_IDENTIFIER>
InChI=1S/C4H6N2/c1-4-5-2-3-6-4/h2-3H,1H3,(H,5,6)

> <INCHI_KEY>
LXBGSDVWAMZHDD-UHFFFAOYSA-N

> <FORMULA>
C4H6N2

> <MOLECULAR_WEIGHT>
82.1038

> <EXACT_MASS>
82.053098202

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
8.73834516065651

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-methyl-1H-imidazole

> <ALOGPS_LOGP>
0.36

> <JCHEM_LOGP>
-0.022159476333333344

> <ALOGPS_LOGS>
0.86

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.924598793717795

> <JCHEM_PKA_STRONGEST_BASIC>
7.516073142342764

> <JCHEM_POLAR_SURFACE_AREA>
28.68

> <JCHEM_REFRACTIVITY>
23.453500000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.93e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1H-imidazole, 2-methyl-

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for NP0045089 (2-Methyl-1H-imidazole)

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PDB for NP0045089 (2-Methyl-1H-imidazole)
HEADER    PROTEIN                                 20-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-20         0                                  
HETATM    1  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -0.186   1.175   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       2.306   1.175   0.000  0.00  0.00           N+0
CONECT    1    4                                                            
CONECT    2    3    5                                                       
CONECT    3    2    6                                                       
CONECT    4    1    5    6                                                  
CONECT    5    2    4                                                       
CONECT    6    3    4                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END

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3D PDB for NP0045089 (2-Methyl-1H-imidazole)
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SMILES for NP0045089 (2-Methyl-1H-imidazole)
CC1=NC=CN1
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INCHI for NP0045089 (2-Methyl-1H-imidazole)
InChI=1S/C4H6N2/c1-4-5-2-3-6-4/h2-3H,1H3,(H,5,6)
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Synonyms
ValueSource
2-Methylimidazole hydrochlorideMeSH
2-Methylimidazole, silver (1+) saltMeSH
ZN(2-Methylimidazole)2MeSH
Chemical FormulaC4H6N2
Average Mass82.1038 Da
Monoisotopic Mass82.05310 Da
IUPAC Name2-methyl-1H-imidazole
Traditional Name1H-imidazole, 2-methyl-
CAS Registry Number693-98-1
SMILES
CC1=NC=CN1
InChI Identifier
InChI=1S/C4H6N2/c1-4-5-2-3-6-4/h2-3H,1H3,(H,5,6)
InChI KeyLXBGSDVWAMZHDD-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Cannabis sativaNULL
      Not Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as imidazoles. Imidazoles are compounds containing an imidazole ring, which is an aromatic five-member ring with two nitrogen atoms at positions 1 and 3, and three carbon atoms.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassAzoles  
Sub ClassImidazoles  
Direct ParentImidazoles  
Alternative Parents
Substituents
  • Heteroaromatic compound
    • 

  • Imidazole
    • 

  • Azacycle
    • 

  • Organic nitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organonitrogen compound
    • 

  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP0.36ALOGPS
logP-0.022ChemAxon
logS0.86ALOGPS
pKa (Strongest Acidic)13.92ChemAxon
pKa (Strongest Basic)7.52ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area28.68 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity23.45 m³·mol⁻¹ChemAxon
Polarizability8.74 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC19261  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound12749  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Rice S, Koziel JA: Characterizing the Smell of Marijuana by Odor Impact of Volatile Compounds: An Application of Simultaneous Chemical and Sensory Analysis. PLoS One. 2015 Dec 10;10(12):e0144160. doi: 10.1371/journal.pone.0144160. eCollection 2015. [PubMed:26657499  ]