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Showing metabocard for 3,6-Dimethylpyrazine-2-thiol (HMDB0246079)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:07:02 UTC
Update Date2021-09-26 22:54:56 UTC
HMDB IDHMDB0246079
Secondary Accession NumbersNone
Metabolite Identification
Common Name3,6-Dimethylpyrazine-2-thiol
Description3,6-Dimethylpyrazine-2-thiol 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 a small amount of articles have been published on 3,6-Dimethylpyrazine-2-thiol. This compound has been identified in human blood as reported by (PMID: 31557052 ). 3,6-dimethylpyrazine-2-thiol is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 3,6-Dimethylpyrazine-2-thiol 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 HMDB0246079 (3,6-Dimethylpyrazine-2-thiol)


  Mrv1652309112101072D          

  9  9  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 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   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 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   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  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
  6  8  1  0  0  0  0
  2  8  1  0  0  0  0
  5  9  1  0  0  0  0
M  END
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3D MOL for HMDB0246079 (3,6-Dimethylpyrazine-2-thiol)

HMDB0246079
     RDKit          3D
3,6-Dimethylpyrazine-2-thiol
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.7969    0.3046   -0.0275 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3296    0.1084   -0.0492 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7839   -0.9132   -0.7930 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5453   -1.1290   -0.8423 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4062   -0.3502   -0.1616 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8781   -0.5736   -0.2040 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8521    0.6729    0.5827 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8843    1.6362    1.4217 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.4751    0.8913    0.6341 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3294   -0.5823    0.4198 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0419    1.1447    0.6793 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2309    0.5610   -0.9916 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4853   -1.5480   -1.3478 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3599    0.2708    0.3414 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2565   -0.6705   -1.2503 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1680   -1.4907    0.3876 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8774    1.6677    1.2006 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
  5  7  1  0
  7  8  2  0
  7  9  1  0
  9  2  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  3 13  1  0
  6 14  1  0
  6 15  1  0
  6 16  1  0
  9 17  1  0
M  END
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3D SDF for HMDB0246079 (3,6-Dimethylpyrazine-2-thiol)


  Mrv1652309112101072D          

  9  9  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 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   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 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   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  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
  6  8  1  0  0  0  0
  2  8  1  0  0  0  0
  5  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0246079

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CN=C(C)C(=S)N1

> <INCHI_IDENTIFIER>
InChI=1S/C6H8N2S/c1-4-3-7-5(2)6(9)8-4/h3H,1-2H3,(H,8,9)

> <INCHI_KEY>
ARBPVCYTFYHIPO-UHFFFAOYSA-N

> <FORMULA>
C6H8N2S

> <MOLECULAR_WEIGHT>
140.2

> <EXACT_MASS>
140.04081944

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
14.898705168212937

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,6-dimethyl-1,2-dihydropyrazine-2-thione

> <ALOGPS_LOGP>
1.05

> <JCHEM_LOGP>
0.7654604953333333

> <ALOGPS_LOGS>
-2.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.92233950243694

> <JCHEM_PKA_STRONGEST_BASIC>
4.575718672395753

> <JCHEM_POLAR_SURFACE_AREA>
24.39

> <JCHEM_REFRACTIVITY>
42.88099999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.61e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,6-dimethyl-1H-pyrazine-2-thione

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0246079 (3,6-Dimethylpyrazine-2-thiol)

HMDB0246079
     RDKit          3D
3,6-Dimethylpyrazine-2-thiol
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.7969    0.3046   -0.0275 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3296    0.1084   -0.0492 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7839   -0.9132   -0.7930 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5453   -1.1290   -0.8423 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4062   -0.3502   -0.1616 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8781   -0.5736   -0.2040 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8521    0.6729    0.5827 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8843    1.6362    1.4217 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.4751    0.8913    0.6341 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3294   -0.5823    0.4198 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0419    1.1447    0.6793 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2309    0.5610   -0.9916 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4853   -1.5480   -1.3478 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3599    0.2708    0.3414 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2565   -0.6705   -1.2503 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1680   -1.4907    0.3876 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8774    1.6677    1.2006 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
  5  7  1  0
  7  8  2  0
  7  9  1  0
  9  2  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  3 13  1  0
  6 14  1  0
  6 15  1  0
  6 16  1  0
  9 17  1  0
M  END
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PDB for HMDB0246079 (3,6-Dimethylpyrazine-2-thiol)

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  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       2.667  -0.000   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  S   UNK     0      -1.334  -0.770   0.000  0.00  0.00           S+0
HETATM    8  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    9                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    2                                                       
CONECT    9    5                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for HMDB0246079 (3,6-Dimethylpyrazine-2-thiol)

COMPND    HMDB0246079
HETATM    1  C1  UNL     1       2.797   0.305  -0.028  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.330   0.108  -0.049  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.784  -0.913  -0.793  1.00  0.00           C  
HETATM    4  N1  UNL     1      -0.545  -1.129  -0.842  1.00  0.00           N  
HETATM    5  C4  UNL     1      -1.406  -0.350  -0.162  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.878  -0.574  -0.204  1.00  0.00           C  
HETATM    7  C6  UNL     1      -0.852   0.673   0.583  1.00  0.00           C  
HETATM    8  S1  UNL     1      -1.884   1.636   1.422  1.00  0.00           S  
HETATM    9  N2  UNL     1       0.475   0.891   0.634  1.00  0.00           N  
HETATM   10  H1  UNL     1       3.329  -0.582   0.420  1.00  0.00           H  
HETATM   11  H2  UNL     1       3.042   1.145   0.679  1.00  0.00           H  
HETATM   12  H3  UNL     1       3.231   0.561  -0.992  1.00  0.00           H  
HETATM   13  H4  UNL     1       1.485  -1.548  -1.348  1.00  0.00           H  
HETATM   14  H5  UNL     1      -3.360   0.271   0.341  1.00  0.00           H  
HETATM   15  H6  UNL     1      -3.256  -0.671  -1.250  1.00  0.00           H  
HETATM   16  H7  UNL     1      -3.168  -1.491   0.388  1.00  0.00           H  
HETATM   17  H8  UNL     1       0.877   1.668   1.201  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3    3    9
CONECT    3    4   13
CONECT    4    5    5
CONECT    5    6    7
CONECT    6   14   15   16
CONECT    7    8    8    9
CONECT    9   17
END
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SMILES for HMDB0246079 (3,6-Dimethylpyrazine-2-thiol)

CC1=CN=C(C)C(=S)N1
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INCHI for HMDB0246079 (3,6-Dimethylpyrazine-2-thiol)

InChI=1S/C6H8N2S/c1-4-3-7-5(2)6(9)8-4/h3H,1-2H3,(H,8,9)
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC6H8N2S
Average Molecular Weight140.2
Monoisotopic Molecular Weight140.04081944
IUPAC Name3,6-dimethyl-1,2-dihydropyrazine-2-thione
Traditional Name3,6-dimethyl-1H-pyrazine-2-thione
CAS Registry NumberNot Available
SMILES
CC1=CN=C(C)C(=S)N1
InChI Identifier
InChI=1S/C6H8N2S/c1-4-3-7-5(2)6(9)8-4/h3H,1-2H3,(H,8,9)
InChI KeyARBPVCYTFYHIPO-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
  • Heteroaromatic compound
  • Thiolactam
  • Azacycle
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organosulfur compound
  • 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
logP1.05ALOGPS
logP0.77ChemAxon
logS-2.6ALOGPS
pKa (Strongest Acidic)9.92ChemAxon
pKa (Strongest Basic)4.58ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area24.39 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity42.88 m³·mol⁻¹ChemAxon
Polarizability14.9 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]+131.35730932474
DeepCCS[M-H]-128.97430932474
DeepCCS[M-2H]-165.34830932474
DeepCCS[M+Na]+140.25530932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3,6-Dimethylpyrazine-2-thiolCC1=CN=C(C)C(=S)N12021.3Standard polar33892256
3,6-Dimethylpyrazine-2-thiolCC1=CN=C(C)C(=S)N11264.8Standard non polar33892256
3,6-Dimethylpyrazine-2-thiolCC1=CN=C(C)C(=S)N11542.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3,6-Dimethylpyrazine-2-thiol,1TMS,isomer #1CC1=NC=C(C)N([Si](C)(C)C)C1=S1485.5Semi standard non polar33892256
3,6-Dimethylpyrazine-2-thiol,1TMS,isomer #1CC1=NC=C(C)N([Si](C)(C)C)C1=S1497.8Standard non polar33892256
3,6-Dimethylpyrazine-2-thiol,1TMS,isomer #1CC1=NC=C(C)N([Si](C)(C)C)C1=S1934.4Standard polar33892256
3,6-Dimethylpyrazine-2-thiol,1TBDMS,isomer #1CC1=NC=C(C)N([Si](C)(C)C(C)(C)C)C1=S1714.6Semi standard non polar33892256
3,6-Dimethylpyrazine-2-thiol,1TBDMS,isomer #1CC1=NC=C(C)N([Si](C)(C)C(C)(C)C)C1=S1726.5Standard non polar33892256
3,6-Dimethylpyrazine-2-thiol,1TBDMS,isomer #1CC1=NC=C(C)N([Si](C)(C)C(C)(C)C)C1=S2041.7Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3,6-Dimethylpyrazine-2-thiol GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-7900000000-359b74b7bc223ee2da4b2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,6-Dimethylpyrazine-2-thiol 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 - 3,6-Dimethylpyrazine-2-thiol 10V, Positive-QTOFsplash10-0006-0900000000-50daad794ed682c6d4cf2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,6-Dimethylpyrazine-2-thiol 20V, Positive-QTOFsplash10-0006-9400000000-533c8fba2ac6c7fa3d5c2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,6-Dimethylpyrazine-2-thiol 40V, Positive-QTOFsplash10-0zfu-9000000000-ddd46ea06a0154a872252021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,6-Dimethylpyrazine-2-thiol 10V, Negative-QTOFsplash10-00ks-9500000000-ee66a256f1fbdd4825122021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,6-Dimethylpyrazine-2-thiol 20V, Negative-QTOFsplash10-0ar9-9100000000-f815527dbea0b37a3df22021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,6-Dimethylpyrazine-2-thiol 40V, Negative-QTOFsplash10-0a4i-9000000000-fa68cb543fdf219097a02021-10-12Wishart 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 ID2300302
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound134594
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 ]