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Showing metabocard for 4-Methylimidazole (HMDB0246511)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:31:43 UTC
Update Date2021-09-26 22:55:39 UTC
HMDB IDHMDB0246511
Secondary Accession NumbersNone
Metabolite Identification
Common Name4-Methylimidazole
Description4-methylimidazole, also known as 4-me-I or 4MI, 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. Based on a literature review a significant number of articles have been published on 4-methylimidazole. This compound has been identified in human blood as reported by (PMID: 31557052 ). 4-methylimidazole is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 4-Methylimidazole is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0246511 (4-Methylimidazole)


  Mrv0541 05031422172D          

  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
    1.2352    0.6294    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
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 N   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
  4  1  1  0  0  0  0
  4  2  2  0  0  0  0
  5  2  1  0  0  0  0
  5  3  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 HMDB0246511 (4-Methylimidazole)

HMDB0246511
     RDKit          3D
4-Methylimidazole
 12 12  0  0  0  0  0  0  0  0999 V2000
    1.6902   -0.2277   -0.1158 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2471    0.1056    0.0062 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3551    1.3140    0.2649 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6782    1.0881    0.2734 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9295   -0.1885    0.0354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7402   -0.7935   -0.1293 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3346    0.5227    0.3893 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8247   -1.2115    0.3979 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9186   -0.3051   -1.1806 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1617    2.2566    0.4275 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8649   -0.7298   -0.0327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6090   -1.8309   -0.3361 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
  3 10  1  0
  5 11  1  0
  6 12  1  0
M  END
Download

3D SDF for HMDB0246511 (4-Methylimidazole)


  Mrv0541 05031422172D          

  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
    1.2352    0.6294    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
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 N   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
  4  1  1  0  0  0  0
  4  2  2  0  0  0  0
  5  2  1  0  0  0  0
  5  3  2  0  0  0  0
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0246511

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CN=CN1

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

> <INCHI_KEY>
XLSZMDLNRCVEIJ-UHFFFAOYSA-N

> <FORMULA>
C4H6N2

> <MOLECULAR_WEIGHT>
82.1038

> <EXACT_MASS>
82.053098202

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
8.642319773100064

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
0.10

> <JCHEM_LOGP>
0.054337116000000005

> <ALOGPS_LOGS>
0.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.776225731132378

> <JCHEM_PKA_STRONGEST_BASIC>
7.493325117110688

> <JCHEM_POLAR_SURFACE_AREA>
28.68

> <JCHEM_REFRACTIVITY>
24.1625

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.78e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-methylimidazole

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0246511 (4-Methylimidazole)

HMDB0246511
     RDKit          3D
4-Methylimidazole
 12 12  0  0  0  0  0  0  0  0999 V2000
    1.6902   -0.2277   -0.1158 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2471    0.1056    0.0062 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3551    1.3140    0.2649 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6782    1.0881    0.2734 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9295   -0.1885    0.0354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7402   -0.7935   -0.1293 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3346    0.5227    0.3893 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8247   -1.2115    0.3979 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9186   -0.3051   -1.1806 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1617    2.2566    0.4275 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8649   -0.7298   -0.0327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6090   -1.8309   -0.3361 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
  3 10  1  0
  5 11  1  0
  6 12  1  0
M  END
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PDB for HMDB0246511 (4-Methylimidazole)

HEADER    PROTEIN                                 03-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   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  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
CONECT    1    4                                                            
CONECT    2    4    5                                                       
CONECT    3    5    6                                                       
CONECT    4    1    2    6                                                  
CONECT    5    2    3                                                       
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 HMDB0246511 (4-Methylimidazole)

COMPND    HMDB0246511
HETATM    1  C1  UNL     1       1.690  -0.228  -0.116  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.247   0.106   0.006  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.355   1.314   0.265  1.00  0.00           C  
HETATM    4  N1  UNL     1      -1.678   1.088   0.273  1.00  0.00           N  
HETATM    5  C4  UNL     1      -1.930  -0.188   0.035  1.00  0.00           C  
HETATM    6  N2  UNL     1      -0.740  -0.794  -0.129  1.00  0.00           N  
HETATM    7  H1  UNL     1       2.335   0.523   0.389  1.00  0.00           H  
HETATM    8  H2  UNL     1       1.825  -1.211   0.398  1.00  0.00           H  
HETATM    9  H3  UNL     1       1.919  -0.305  -1.181  1.00  0.00           H  
HETATM   10  H4  UNL     1       0.162   2.257   0.428  1.00  0.00           H  
HETATM   11  H5  UNL     1      -2.865  -0.730  -0.033  1.00  0.00           H  
HETATM   12  H6  UNL     1      -0.609  -1.831  -0.336  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3    3    6
CONECT    3    4   10
CONECT    4    5    5
CONECT    5    6   11
CONECT    6   12
END
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SMILES for HMDB0246511 (4-Methylimidazole)

CC1=CN=CN1
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INCHI for HMDB0246511 (4-Methylimidazole)

InChI=1S/C4H6N2/c1-4-2-5-3-6-4/h2-3H,1H3,(H,5,6)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
4(5)-MethylimidazoleChEBI
4-Me-iChEBI
4-MEIChEBI
4MIChEBI
4-Methylimidazole oxalate (1:1)MeSH
4-Methylimidazole, ion(1-)MeSH
4-Methylimidazole hydrideMeSH
5-MethylimidazoleMeSH
Chemical FormulaC4H6N2
Average Molecular Weight82.1038
Monoisotopic Molecular Weight82.053098202
IUPAC Name5-methyl-1H-imidazole
Traditional Name4-methylimidazole
CAS Registry NumberNot Available
SMILES
CC1=CN=CN1
InChI Identifier
InChI=1S/C4H6N2/c1-4-2-5-3-6-4/h2-3H,1H3,(H,5,6)
InChI KeyXLSZMDLNRCVEIJ-UHFFFAOYSA-N
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 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
logP0.1ALOGPS
logP0.054ChemAxon
logS0.85ALOGPS
pKa (Strongest Acidic)13.78ChemAxon
pKa (Strongest Basic)7.49ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area28.68 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity24.16 m³·mol⁻¹ChemAxon
Polarizability8.64 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]+116.84430932474
DeepCCS[M-H]-114.83930932474
DeepCCS[M-2H]-150.50530932474
DeepCCS[M+Na]+125.01730932474
AllCCS[M+H]+116.332859911
AllCCS[M+H-H2O]+111.032859911
AllCCS[M+NH4]+121.232859911
AllCCS[M+Na]+122.632859911
AllCCS[M-H]-117.232859911
AllCCS[M+Na-2H]-121.132859911
AllCCS[M+HCOO]-125.332859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20228.0937 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.46 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid491.0 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid327.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid82.3 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid232.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid66.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid263.1 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 Acid255.9 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)553.0 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid555.1 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid38.0 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid655.0 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid204.0 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid289.6 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate575.7 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA380.4 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water277.2 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
4-MethylimidazoleCC1=CN=CN12146.4Standard polar33892256
4-MethylimidazoleCC1=CN=CN11021.1Standard non polar33892256
4-MethylimidazoleCC1=CN=CN11066.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
4-Methylimidazole,1TMS,isomer #1CC1=CN=CN1[Si](C)(C)C1158.4Semi standard non polar33892256
4-Methylimidazole,1TMS,isomer #1CC1=CN=CN1[Si](C)(C)C1094.8Standard non polar33892256
4-Methylimidazole,1TMS,isomer #1CC1=CN=CN1[Si](C)(C)C1379.8Standard polar33892256
4-Methylimidazole,1TBDMS,isomer #1CC1=CN=CN1[Si](C)(C)C(C)(C)C1391.4Semi standard non polar33892256
4-Methylimidazole,1TBDMS,isomer #1CC1=CN=CN1[Si](C)(C)C(C)(C)C1284.2Standard non polar33892256
4-Methylimidazole,1TBDMS,isomer #1CC1=CN=CN1[Si](C)(C)C(C)(C)C1518.8Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 4-Methylimidazole GC-MS (Non-derivatized) - 70eV, Positivesplash10-001i-9000000000-f907a0f4061c7d7e89362021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 4-Methylimidazole 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 - 4-Methylimidazole 10V, Positive-QTOFsplash10-001i-9000000000-0a5589455807221a26b62016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylimidazole 20V, Positive-QTOFsplash10-053r-9000000000-b0a507a812d0c9f4652a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylimidazole 40V, Positive-QTOFsplash10-0gb9-9000000000-fd7fd99f7ffda0bc0ef32016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylimidazole 10V, Negative-QTOFsplash10-001i-9000000000-5bba7c210ef14fb1b3902016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylimidazole 20V, Negative-QTOFsplash10-001i-9000000000-ce0b6bfe4d9793f91e7d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylimidazole 40V, Negative-QTOFsplash10-0udi-9000000000-a04da93efdb8dc6397cc2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylimidazole 10V, Positive-QTOFsplash10-001i-9000000000-1cf93dacee6d717174102021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylimidazole 20V, Positive-QTOFsplash10-0a4i-9000000000-db90b9b685a8dfd2e8172021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylimidazole 40V, Positive-QTOFsplash10-0pb9-9000000000-21b1b904186893c322f32021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylimidazole 10V, Negative-QTOFsplash10-001i-9000000000-5fba3d16c726bdbb206a2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylimidazole 20V, Negative-QTOFsplash10-001i-9000000000-2c5ebba55efa7cda1e972021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Methylimidazole 40V, Negative-QTOFsplash10-014l-9000000000-733f4e5972d8d92f09432021-10-12Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID12640
KEGG Compound IDC19262
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link4-Methylimidazole
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID40035
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1205101
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]