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Showing metabocard for 2-Methylimidazole (HMDB0245233)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:19:26 UTC
Update Date2021-09-26 22:53:34 UTC
HMDB IDHMDB0245233
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-Methylimidazole
Description2-Methylimidazole 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 very few articles have been published on 2-Methylimidazole. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2-methylimidazole is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2-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 HMDB0245233 (2-Methylimidazole)


  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
Download

3D MOL for HMDB0245233 (2-Methylimidazole)

HMDB0245233
     RDKit          3D
2-Methylimidazole
 12 12  0  0  0  0  0  0  0  0999 V2000
   -1.9322   -0.1736    0.0855 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4303   -0.1588    0.0171 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3980   -1.2169   -0.0037 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6794   -0.8164   -0.0682 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6692    0.5621   -0.0896 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3736    0.9175   -0.0364 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2412   -1.1996   -0.2090 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2795   -0.0629    1.1497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3859    0.5765   -0.5720 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5468   -1.4909   -0.0968 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5699    1.1579   -0.1399 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0322    1.9052   -0.0366 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
Download

3D SDF for HMDB0245233 (2-Methylimidazole)


  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>
HMDB0245233

> <DATABASE_NAME>
hmdb

> <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

$$$$
Download

3D-SDF for HMDB0245233 (2-Methylimidazole)

HMDB0245233
     RDKit          3D
2-Methylimidazole
 12 12  0  0  0  0  0  0  0  0999 V2000
   -1.9322   -0.1736    0.0855 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4303   -0.1588    0.0171 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3980   -1.2169   -0.0037 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6794   -0.8164   -0.0682 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6692    0.5621   -0.0896 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3736    0.9175   -0.0364 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2412   -1.1996   -0.2090 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2795   -0.0629    1.1497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3859    0.5765   -0.5720 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5468   -1.4909   -0.0968 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5699    1.1579   -0.1399 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0322    1.9052   -0.0366 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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PDB for HMDB0245233 (2-Methylimidazole)

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 HMDB0245233 (2-Methylimidazole)

COMPND    HMDB0245233
HETATM    1  C1  UNL     1      -1.932  -0.174   0.085  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.430  -0.159   0.017  1.00  0.00           C  
HETATM    3  N1  UNL     1       0.398  -1.217  -0.004  1.00  0.00           N  
HETATM    4  C3  UNL     1       1.679  -0.816  -0.068  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.669   0.562  -0.090  1.00  0.00           C  
HETATM    6  N2  UNL     1       0.374   0.917  -0.036  1.00  0.00           N  
HETATM    7  H1  UNL     1      -2.241  -1.200  -0.209  1.00  0.00           H  
HETATM    8  H2  UNL     1      -2.280  -0.063   1.150  1.00  0.00           H  
HETATM    9  H3  UNL     1      -2.386   0.576  -0.572  1.00  0.00           H  
HETATM   10  H4  UNL     1       2.547  -1.491  -0.097  1.00  0.00           H  
HETATM   11  H5  UNL     1       2.570   1.158  -0.140  1.00  0.00           H  
HETATM   12  H6  UNL     1       0.032   1.905  -0.037  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3    3    6
CONECT    3    4
CONECT    4    5    5   10
CONECT    5    6   11
CONECT    6   12
END
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SMILES for HMDB0245233 (2-Methylimidazole)

CC1=NC=CN1
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INCHI for HMDB0245233 (2-Methylimidazole)

InChI=1S/C4H6N2/c1-4-5-2-3-6-4/h2-3H,1H3,(H,5,6)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-Methylimidazole hydrochlorideHMDB
2-Methylimidazole, silver (1+) saltHMDB
ZN(2-Methylimidazole)2HMDB
Chemical FormulaC4H6N2
Average Molecular Weight82.1038
Monoisotopic Molecular Weight82.053098202
IUPAC Name2-methyl-1H-imidazole
Traditional Name1H-imidazole, 2-methyl-
CAS Registry NumberNot Available
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
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
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
logP0.36ALOGPS
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
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+118.22530932474
DeepCCS[M-H]-116.25830932474
DeepCCS[M-2H]-151.94630932474
DeepCCS[M+Na]+126.46830932474
AllCCS[M+H]+117.632859911
AllCCS[M+H-H2O]+112.432859911
AllCCS[M+NH4]+122.432859911
AllCCS[M+Na]+123.832859911
AllCCS[M-H]-117.232859911
AllCCS[M+Na-2H]-121.032859911
AllCCS[M+HCOO]-125.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-MethylimidazoleCC1=NC=CN12054.3Standard polar33892256
2-MethylimidazoleCC1=NC=CN1982.0Standard non polar33892256
2-MethylimidazoleCC1=NC=CN11027.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-Methylimidazole,1TMS,isomer #1CC1=NC=CN1[Si](C)(C)C1150.9Semi standard non polar33892256
2-Methylimidazole,1TMS,isomer #1CC1=NC=CN1[Si](C)(C)C1070.0Standard non polar33892256
2-Methylimidazole,1TMS,isomer #1CC1=NC=CN1[Si](C)(C)C1347.1Standard polar33892256
2-Methylimidazole,1TBDMS,isomer #1CC1=NC=CN1[Si](C)(C)C(C)(C)C1371.5Semi standard non polar33892256
2-Methylimidazole,1TBDMS,isomer #1CC1=NC=CN1[Si](C)(C)C(C)(C)C1258.6Standard non polar33892256
2-Methylimidazole,1TBDMS,isomer #1CC1=NC=CN1[Si](C)(C)C(C)(C)C1486.1Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2-Methylimidazole GC-MS (Non-derivatized) - 70eV, PositiveNot Available2020-06-30Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Methylimidazole GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - 2-Methylimidazole LC-ESI-QFT 5V, positive-QTOFsplash10-001i-9000000000-e4f7fea4cd54cb30a9eb2020-07-21HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 2-Methylimidazole 150V, Positive-QTOFsplash10-001i-9000000000-e4f7fea4cd54cb30a9eb2021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylimidazole 10V, Positive-QTOFsplash10-001i-9000000000-4e3785e565516e68dc352016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylimidazole 20V, Positive-QTOFsplash10-001i-9000000000-a6a0a295e7fc4c2f101d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylimidazole 40V, Positive-QTOFsplash10-0aou-9000000000-216aecf6a69f53d16f7b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylimidazole 10V, Negative-QTOFsplash10-001i-9000000000-c42fcd9a6442fc5da0cb2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylimidazole 20V, Negative-QTOFsplash10-001i-9000000000-f37830ccb1cef86f29422016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylimidazole 40V, Negative-QTOFsplash10-0006-9000000000-c1c8bc19b2db2bff6d252016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylimidazole 10V, Positive-QTOFsplash10-001i-9000000000-0c4ca615527c02a811972021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylimidazole 20V, Positive-QTOFsplash10-0api-9000000000-59d4b654c5e576d17af92021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylimidazole 40V, Positive-QTOFsplash10-0a4i-9000000000-9fefb19eb2dbfb5b97422021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylimidazole 10V, Negative-QTOFsplash10-001i-9000000000-5fba3d16c726bdbb206a2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylimidazole 20V, Negative-QTOFsplash10-0a4i-9000000000-e522e427b7835934ef5f2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylimidazole 40V, Negative-QTOFsplash10-01ox-9000000000-9822d44a57700c61f65c2021-10-12Wishart 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 ID12225
KEGG Compound IDC19261
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link2-Methylimidazole
METLIN IDNot Available
PubChem Compound12749
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1179121
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 ]