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Showing metabocard for 2-Chloro-3-methylpyrazine (HMDB0245051)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:09:38 UTC
Update Date2021-09-26 22:53:14 UTC
HMDB IDHMDB0245051
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-Chloro-3-methylpyrazine
Description2-Chloro-3-methylpyrazine, also known as (1-3,1-6)-beta-glucan or ha-beta-glucan, belongs to the class of organic compounds known as pyrazines. Pyrazines are compounds containing a pyrazine ring, which is a six-member aromatic heterocycle, that consists of two nitrogen atoms (at positions 1 and 4) and four carbon atoms. Based on a literature review very few articles have been published on 2-Chloro-3-methylpyrazine. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2-chloro-3-methylpyrazine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2-Chloro-3-methylpyrazine 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 HMDB0245051 (2-Chloro-3-methylpyrazine)


  Mrv1652309112100092D          

  8  8  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    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   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
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   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 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
M  END
Download

3D MOL for HMDB0245051 (2-Chloro-3-methylpyrazine)

HMDB0245051
     RDKit          3D
2-Chloro-3-methylpyrazine
 13 13  0  0  0  0  0  0  0  0999 V2000
    2.0325   -0.3428   -0.0945 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5551   -0.1542   -0.0528 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3064   -1.1030   -0.4682 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6365   -0.8705   -0.4046 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1680    0.3100    0.0726 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3078    1.2580    0.4877 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0322    1.0252    0.4242 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1563    2.2627    0.9661 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.3621   -0.7367    0.8890 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5625    0.6159   -0.3311 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3291   -1.0822   -0.8535 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3608   -1.6276   -0.7370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2503    0.4451    0.1019 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  8  1  0
  7  2  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  4 12  1  0
  5 13  1  0
M  END
Download

3D SDF for HMDB0245051 (2-Chloro-3-methylpyrazine)


  Mrv1652309112100092D          

  8  8  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    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   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
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   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 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245051

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=NC=CN=C1Cl

> <INCHI_IDENTIFIER>
InChI=1S/C5H5ClN2/c1-4-5(6)8-3-2-7-4/h2-3H,1H3

> <INCHI_KEY>
WZHWPZQQPWKEAV-UHFFFAOYSA-N

> <FORMULA>
C5H5ClN2

> <MOLECULAR_WEIGHT>
128.56

> <EXACT_MASS>
128.0141259

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
11.843138427613486

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-chloro-3-methylpyrazine

> <ALOGPS_LOGP>
1.06

> <JCHEM_LOGP>
0.49349298433333333

> <ALOGPS_LOGS>
-0.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
0.6230054829909115

> <JCHEM_POLAR_SURFACE_AREA>
25.78

> <JCHEM_REFRACTIVITY>
32.2018

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.04e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-chloro-3-methylpyrazine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0245051 (2-Chloro-3-methylpyrazine)

HMDB0245051
     RDKit          3D
2-Chloro-3-methylpyrazine
 13 13  0  0  0  0  0  0  0  0999 V2000
    2.0325   -0.3428   -0.0945 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5551   -0.1542   -0.0528 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3064   -1.1030   -0.4682 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6365   -0.8705   -0.4046 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1680    0.3100    0.0726 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3078    1.2580    0.4877 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0322    1.0252    0.4242 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1563    2.2627    0.9661 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.3621   -0.7367    0.8890 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5625    0.6159   -0.3311 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3291   -1.0822   -0.8535 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3608   -1.6276   -0.7370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2503    0.4451    0.1019 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  8  1  0
  7  2  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  4 12  1  0
  5 13  1  0
M  END
Download

PDB for HMDB0245051 (2-Chloro-3-methylpyrazine)

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       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    8 Cl   UNK     0      -1.334   2.310   0.000  0.00  0.00          Cl+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    2    8                                                  
CONECT    8    7                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0245051 (2-Chloro-3-methylpyrazine)

COMPND    HMDB0245051
HETATM    1  C1  UNL     1       2.033  -0.343  -0.094  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.555  -0.154  -0.053  1.00  0.00           C  
HETATM    3  N1  UNL     1      -0.306  -1.103  -0.468  1.00  0.00           N  
HETATM    4  C3  UNL     1      -1.637  -0.871  -0.405  1.00  0.00           C  
HETATM    5  C4  UNL     1      -2.168   0.310   0.073  1.00  0.00           C  
HETATM    6  N2  UNL     1      -1.308   1.258   0.488  1.00  0.00           N  
HETATM    7  C5  UNL     1       0.032   1.025   0.424  1.00  0.00           C  
HETATM    8 CL1  UNL     1       1.156   2.263   0.966  1.00  0.00          CL  
HETATM    9  H1  UNL     1       2.362  -0.737   0.889  1.00  0.00           H  
HETATM   10  H2  UNL     1       2.562   0.616  -0.331  1.00  0.00           H  
HETATM   11  H3  UNL     1       2.329  -1.082  -0.853  1.00  0.00           H  
HETATM   12  H4  UNL     1      -2.361  -1.628  -0.737  1.00  0.00           H  
HETATM   13  H5  UNL     1      -3.250   0.445   0.102  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3    3    7
CONECT    3    4
CONECT    4    5    5   12
CONECT    5    6   13
CONECT    6    7    7
CONECT    7    8
END
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SMILES for HMDB0245051 (2-Chloro-3-methylpyrazine)

CC1=NC=CN=C1Cl
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INCHI for HMDB0245051 (2-Chloro-3-methylpyrazine)

InChI=1S/C5H5ClN2/c1-4-5(6)8-3-2-7-4/h2-3H,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(1-3)-beta-D,(1-6)-beta-D-GlucanMeSH
(1-3,1-6)-beta-GlucanMeSH
HA-beta-glucanMeSH
beta-(1-3)-(1-6)-GlucanMeSH
beta-1,3-beta-1,6-GlucanMeSH
beta-Glucan, (1-3)(1-6)MeSH
CinereanMeSH
EpiglucanMeSH
TranslamMeSH
Chemical FormulaC5H5ClN2
Average Molecular Weight128.56
Monoisotopic Molecular Weight128.0141259
IUPAC Name2-chloro-3-methylpyrazine
Traditional Name2-chloro-3-methylpyrazine
CAS Registry NumberNot Available
SMILES
CC1=NC=CN=C1Cl
InChI Identifier
InChI=1S/C5H5ClN2/c1-4-5(6)8-3-2-7-4/h2-3H,1H3
InChI KeyWZHWPZQQPWKEAV-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrazines. Pyrazines are compounds containing a pyrazine ring, which is a six-member aromatic heterocycle, that consists of two nitrogen atoms (at positions 1 and 4) and four carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrazines
Direct ParentPyrazines
Alternative Parents
Substituents
  • Pyrazine
  • Aryl halide
  • Aryl chloride
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Organochloride
  • Organohalogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot 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
logP1.06ALOGPS
logP0.49ChemAxon
logS-0.09ALOGPS
pKa (Strongest Basic)0.62ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area25.78 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity32.2 m³·mol⁻¹ChemAxon
Polarizability11.84 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]+125.84530932474
DeepCCS[M-H]-123.79230932474
DeepCCS[M-2H]-159.68530932474
DeepCCS[M+Na]+134.38530932474
AllCCS[M+H]+125.832859911
AllCCS[M+H-H2O]+120.932859911
AllCCS[M+NH4]+130.332859911
AllCCS[M+Na]+131.632859911
AllCCS[M-H]-122.832859911
AllCCS[M+Na-2H]-125.532859911
AllCCS[M+HCOO]-128.432859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-Chloro-3-methylpyrazineCC1=NC=CN=C1Cl1400.8Standard polar33892256
2-Chloro-3-methylpyrazineCC1=NC=CN=C1Cl932.6Standard non polar33892256
2-Chloro-3-methylpyrazineCC1=NC=CN=C1Cl1014.5Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2-Chloro-3-methylpyrazine GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-9600000000-485f0ad099c690e39d0b2021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Chloro-3-methylpyrazine 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-Chloro-3-methylpyrazine 10V, Positive-QTOFsplash10-004i-0900000000-0c89b4f221026d0a18f82021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Chloro-3-methylpyrazine 20V, Positive-QTOFsplash10-004i-1900000000-29832073173ce0eb79162021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Chloro-3-methylpyrazine 40V, Positive-QTOFsplash10-0udi-9100000000-6f1fb6dfa4479199fb622021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Chloro-3-methylpyrazine 10V, Negative-QTOFsplash10-004i-0900000000-252bf76c6ac3f96c31e62021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Chloro-3-methylpyrazine 20V, Negative-QTOFsplash10-004i-0900000000-252bf76c6ac3f96c31e62021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Chloro-3-methylpyrazine 40V, Negative-QTOFsplash10-000x-9000000000-c7aafdd1f8b03957bdf12021-10-12Wishart 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 ID60135
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound66769
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 ]