Hmdb loader

Showing metabocard for 2-(Methylthio)-1H-imidazole (HMDB0244948)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:04:04 UTC
Update Date2021-09-26 22:53:04 UTC
HMDB IDHMDB0244948
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-(Methylthio)-1H-imidazole
Description2-(methylsulfanyl)-1H-imidazole belongs to the class of organic compounds known as aryl thioethers. These are organosulfur compounds containing a thioether group that is substituted by an aryl group. Based on a literature review very few articles have been published on 2-(methylsulfanyl)-1H-imidazole. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2-(methylthio)-1h-imidazole is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2-(Methylthio)-1H-imidazole 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
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0244948 (2-(Methylthio)-1H-imidazole)


  Mrv1652309112100042D          

  7  7  0  0  0  0            999 V2000
   -0.1467    2.3518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 S   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
    1.2352    0.6294    0.0000 N   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
    0.1553   -0.1553    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  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  3  7  1  0  0  0  0
M  END
Download

3D MOL for HMDB0244948 (2-(Methylthio)-1H-imidazole)

HMDB0244948
     RDKit          3D
2-(Methylthio)-1H-imidazole
 13 13  0  0  0  0  0  0  0  0999 V2000
    2.6437   -0.1737    0.4417 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5750    0.2272   -0.9876 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1388   -0.0007   -0.4781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8720   -1.1248   -0.5651 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1070   -0.8846   -0.0777 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1535    0.4394    0.3313 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9321    0.9381    0.0681 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3110   -1.0999    0.9447 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6770   -0.2770    0.0427 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5733    0.6427    1.1799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9552   -1.5725    0.0036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0046    0.9713    0.7760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6168    1.9146    0.2520 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  3  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  5 11  1  0
  6 12  1  0
  7 13  1  0
M  END
Download

3D SDF for HMDB0244948 (2-(Methylthio)-1H-imidazole)


  Mrv1652309112100042D          

  7  7  0  0  0  0            999 V2000
   -0.1467    2.3518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 S   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
    1.2352    0.6294    0.0000 N   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
    0.1553   -0.1553    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  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  3  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0244948

> <DATABASE_NAME>
hmdb

> <SMILES>
CSC1=NC=CN1

> <INCHI_IDENTIFIER>
InChI=1S/C4H6N2S/c1-7-4-5-2-3-6-4/h2-3H,1H3,(H,5,6)

> <INCHI_KEY>
SVOCLWUDDWXHFW-UHFFFAOYSA-N

> <FORMULA>
C4H6N2S

> <MOLECULAR_WEIGHT>
114.17

> <EXACT_MASS>
114.025169375

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
11.62755904162968

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(methylsulfanyl)-1H-imidazole

> <ALOGPS_LOGP>
0.47

> <JCHEM_LOGP>
1.1672429363333334

> <ALOGPS_LOGS>
-0.31

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.663561055421095

> <JCHEM_PKA_STRONGEST_BASIC>
5.437981891996329

> <JCHEM_POLAR_SURFACE_AREA>
28.68

> <JCHEM_REFRACTIVITY>
31.245

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.54e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(methylsulfanyl)-1H-imidazole

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0244948 (2-(Methylthio)-1H-imidazole)

HMDB0244948
     RDKit          3D
2-(Methylthio)-1H-imidazole
 13 13  0  0  0  0  0  0  0  0999 V2000
    2.6437   -0.1737    0.4417 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5750    0.2272   -0.9876 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1388   -0.0007   -0.4781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8720   -1.1248   -0.5651 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1070   -0.8846   -0.0777 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1535    0.4394    0.3313 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9321    0.9381    0.0681 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3110   -1.0999    0.9447 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6770   -0.2770    0.0427 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5733    0.6427    1.1799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9552   -1.5725    0.0036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0046    0.9713    0.7760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6168    1.9146    0.2520 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  3  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  5 11  1  0
  6 12  1  0
  7 13  1  0
M  END
Download

PDB for HMDB0244948 (2-(Methylthio)-1H-imidazole)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0      -0.274   4.390   0.000  0.00  0.00           C+0
HETATM    2  S   UNK     0       1.060   3.620   0.000  0.00  0.00           S+0
HETATM    3  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       2.306   1.175   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -0.186   1.175   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    3                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
Download

3D PDB for HMDB0244948 (2-(Methylthio)-1H-imidazole)

COMPND    HMDB0244948
HETATM    1  C1  UNL     1       2.644  -0.174   0.442  1.00  0.00           C  
HETATM    2  S1  UNL     1       1.575   0.227  -0.988  1.00  0.00           S  
HETATM    3  C2  UNL     1      -0.139  -0.001  -0.478  1.00  0.00           C  
HETATM    4  N1  UNL     1      -0.872  -1.125  -0.565  1.00  0.00           N  
HETATM    5  C3  UNL     1      -2.107  -0.885  -0.078  1.00  0.00           C  
HETATM    6  C4  UNL     1      -2.154   0.439   0.331  1.00  0.00           C  
HETATM    7  N2  UNL     1      -0.932   0.938   0.068  1.00  0.00           N  
HETATM    8  H1  UNL     1       2.311  -1.100   0.945  1.00  0.00           H  
HETATM    9  H2  UNL     1       3.677  -0.277   0.043  1.00  0.00           H  
HETATM   10  H3  UNL     1       2.573   0.643   1.180  1.00  0.00           H  
HETATM   11  H4  UNL     1      -2.955  -1.572   0.004  1.00  0.00           H  
HETATM   12  H5  UNL     1      -3.005   0.971   0.776  1.00  0.00           H  
HETATM   13  H6  UNL     1      -0.617   1.915   0.252  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3
CONECT    3    4    4    7
CONECT    4    5
CONECT    5    6    6   11
CONECT    6    7   12
CONECT    7   13
END
Download

SMILES for HMDB0244948 (2-(Methylthio)-1H-imidazole)

CSC1=NC=CN1
Download

INCHI for HMDB0244948 (2-(Methylthio)-1H-imidazole)

InChI=1S/C4H6N2S/c1-7-4-5-2-3-6-4/h2-3H,1H3,(H,5,6)
Download
View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-(Methylsulphanyl)-1H-imidazoleGenerator
Chemical FormulaC4H6N2S
Average Molecular Weight114.17
Monoisotopic Molecular Weight114.025169375
IUPAC Name2-(methylsulfanyl)-1H-imidazole
Traditional Name2-(methylsulfanyl)-1H-imidazole
CAS Registry NumberNot Available
SMILES
CSC1=NC=CN1
InChI Identifier
InChI=1S/C4H6N2S/c1-7-4-5-2-3-6-4/h2-3H,1H3,(H,5,6)
InChI KeySVOCLWUDDWXHFW-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as aryl thioethers. These are organosulfur compounds containing a thioether group that is substituted by an aryl group.
KingdomOrganic compounds
Super ClassOrganosulfur compounds
ClassThioethers
Sub ClassAryl thioethers
Direct ParentAryl thioethers
Alternative Parents
Substituents
  • Aryl thioether
  • Alkylarylthioether
  • Heteroaromatic compound
  • Imidazole
  • Azole
  • Azacycle
  • Organoheterocyclic compound
  • Sulfenyl compound
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological location
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
logP0.47ALOGPS
logP1.17ChemAxon
logS-0.31ALOGPS
pKa (Strongest Acidic)11.66ChemAxon
pKa (Strongest Basic)5.44ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area28.68 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity31.24 m³·mol⁻¹ChemAxon
Polarizability11.63 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]+122.81330932474
DeepCCS[M-H]-120.63130932474
DeepCCS[M-2H]-156.45130932474
DeepCCS[M+Na]+130.89330932474
AllCCS[M+H]+123.732859911
AllCCS[M+H-H2O]+118.932859911
AllCCS[M+NH4]+128.232859911
AllCCS[M+Na]+129.532859911
AllCCS[M-H]-123.732859911
AllCCS[M+Na-2H]-126.932859911
AllCCS[M+HCOO]-130.432859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-(Methylthio)-1H-imidazoleCSC1=NC=CN11650.9Standard polar33892256
2-(Methylthio)-1H-imidazoleCSC1=NC=CN11082.1Standard non polar33892256
2-(Methylthio)-1H-imidazoleCSC1=NC=CN11280.9Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-(Methylthio)-1H-imidazole,1TMS,isomer #1CSC1=NC=CN1[Si](C)(C)C1356.5Semi standard non polar33892256
2-(Methylthio)-1H-imidazole,1TMS,isomer #1CSC1=NC=CN1[Si](C)(C)C1204.4Standard non polar33892256
2-(Methylthio)-1H-imidazole,1TMS,isomer #1CSC1=NC=CN1[Si](C)(C)C1648.4Standard polar33892256
2-(Methylthio)-1H-imidazole,1TBDMS,isomer #1CSC1=NC=CN1[Si](C)(C)C(C)(C)C1591.8Semi standard non polar33892256
2-(Methylthio)-1H-imidazole,1TBDMS,isomer #1CSC1=NC=CN1[Si](C)(C)C(C)(C)C1443.9Standard non polar33892256
2-(Methylthio)-1H-imidazole,1TBDMS,isomer #1CSC1=NC=CN1[Si](C)(C)C(C)(C)C1784.3Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2-(Methylthio)-1H-imidazole GC-MS (Non-derivatized) - 70eV, Positivesplash10-03dj-9400000000-c9bbcd983375c6f1c0082021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-(Methylthio)-1H-imidazole 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 - 2-(Methylthio)-1H-imidazole 10V, Positive-QTOFsplash10-014i-0900000000-619a04acecbc83bcf3202021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-(Methylthio)-1H-imidazole 20V, Positive-QTOFsplash10-014i-6900000000-bbe4738957f8649141552021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-(Methylthio)-1H-imidazole 40V, Positive-QTOFsplash10-022c-9000000000-4e4e293dd7fad97fbf372021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-(Methylthio)-1H-imidazole 10V, Negative-QTOFsplash10-03di-2900000000-26f9f9983f3d619127c52021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-(Methylthio)-1H-imidazole 20V, Negative-QTOFsplash10-03di-6900000000-fad78e8e466f922ee6262021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-(Methylthio)-1H-imidazole 40V, Negative-QTOFsplash10-0006-9000000000-ec56aef28417328e21aa2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-12Wishart 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 ID118678
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound134652
PDB IDNot Available
ChEBI IDNot Available
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 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 ]