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Showing metabocard for 2-Methoxy-3-methylpyrazine (HMDB0031852)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:45:58 UTC
Update Date2023-02-21 17:21:23 UTC
HMDB IDHMDB0031852
Secondary Accession Numbers
  • HMDB31852
Metabolite Identification
Common Name2-Methoxy-3-methylpyrazine
Description2-Methoxy-3-methylpyrazine belongs to the class of organic compounds known as methoxypyrazines. These are pyrazines containing a methoxyl group attached to the pyrazine ring. 2-Methoxy-3-methylpyrazine has been detected, but not quantified in, burdocks (Arctium lappa) and fenugreeks (Trigonella foenum-graecum). This could make 2-methoxy-3-methylpyrazine a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 2-Methoxy-3-methylpyrazine.
Structure
Data?1677000083
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0031852 (2-Methoxy-3-methylpyrazine)


  Mrv1652304272018432D          

  9  9  0  0  0  0            999 V2000
   -0.8250    1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0
  2  9  1  0  0  0  0
  3  4  2  0  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  6  8  2  0  0  0  0
  6  9  1  0  0  0  0
M  END
Download

3D MOL for HMDB0031852 (2-Methoxy-3-methylpyrazine)

HMDB0031852
     RDKit          3D
2-Methoxy-3-methylpyrazine
 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.2974    1.3680   -0.5373 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5223    0.2641   -0.2227 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1528    0.2411   -0.0659 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6415    1.3153   -0.2002 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9873    1.2354   -0.0342 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5650    0.0422    0.2770 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7949   -1.0567    0.4190 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4463   -0.9533    0.2479 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3861   -2.1668    0.4067 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9250    1.2610   -1.4426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6391    2.2714   -0.6207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9720    1.5659    0.3451 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6305    2.0997   -0.1418 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6283   -0.0553    0.4152 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1029   -2.9568    1.0046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3402   -1.9065    0.9032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5618   -2.5687   -0.6305 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  8  2  0
  8  9  1  0
  8  3  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  5 13  1  0
  6 14  1  0
  9 15  1  0
  9 16  1  0
  9 17  1  0
M  END
Download

3D SDF for HMDB0031852 (2-Methoxy-3-methylpyrazine)


  Mrv1652304272018432D          

  9  9  0  0  0  0            999 V2000
   -0.8250    1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0
  2  9  1  0  0  0  0
  3  4  2  0  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  6  8  2  0  0  0  0
  6  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0031852

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=NC=CN=C1C

> <INCHI_IDENTIFIER>
InChI=1S/C6H8N2O/c1-5-6(9-2)8-4-3-7-5/h3-4H,1-2H3

> <INCHI_KEY>
VKJIAEQRKBQLLA-UHFFFAOYSA-N

> <FORMULA>
C6H8N2O

> <MOLECULAR_WEIGHT>
124.1405

> <EXACT_MASS>
124.063662888

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
12.576803971982622

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-methoxy-3-methylpyrazine

> <ALOGPS_LOGP>
1.09

> <JCHEM_LOGP>
0.10605739533333315

> <ALOGPS_LOGS>
0.24

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
1.2067085488119742

> <JCHEM_POLAR_SURFACE_AREA>
35.010000000000005

> <JCHEM_REFRACTIVITY>
33.112399999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.13e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyrazine, 2-methoxy-3-methyl-

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0031852 (2-Methoxy-3-methylpyrazine)

HMDB0031852
     RDKit          3D
2-Methoxy-3-methylpyrazine
 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.2974    1.3680   -0.5373 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5223    0.2641   -0.2227 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1528    0.2411   -0.0659 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6415    1.3153   -0.2002 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9873    1.2354   -0.0342 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5650    0.0422    0.2770 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7949   -1.0567    0.4190 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4463   -0.9533    0.2479 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3861   -2.1668    0.4067 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9250    1.2610   -1.4426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6391    2.2714   -0.6207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9720    1.5659    0.3451 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6305    2.0997   -0.1418 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6283   -0.0553    0.4152 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1029   -2.9568    1.0046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3402   -1.9065    0.9032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5618   -2.5687   -0.6305 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  8  2  0
  8  9  1  0
  8  3  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  5 13  1  0
  6 14  1  0
  9 15  1  0
  9 16  1  0
  9 17  1  0
M  END
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PDB for HMDB0031852 (2-Methoxy-3-methylpyrazine)

HEADER    PROTEIN                                 27-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-APR-20         0                                  
HETATM    1  C   UNK     0      -1.540   2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.540   0.000   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       0.770   1.334   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0      -0.770  -1.334   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0      -3.080   0.000   0.000  0.00  0.00           O+0
CONECT    1    5                                                            
CONECT    2    9                                                            
CONECT    3    4    7                                                       
CONECT    4    3    8                                                       
CONECT    5    1    6    7                                                  
CONECT    6    5    8    9                                                  
CONECT    7    3    5                                                       
CONECT    8    4    6                                                       
CONECT    9    2    6                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
Download

3D PDB for HMDB0031852 (2-Methoxy-3-methylpyrazine)

COMPND    HMDB0031852
HETATM    1  C1  UNL     1      -2.297   1.368  -0.537  1.00  0.00           C  
HETATM    2  O1  UNL     1      -1.522   0.264  -0.223  1.00  0.00           O  
HETATM    3  C2  UNL     1      -0.153   0.241  -0.066  1.00  0.00           C  
HETATM    4  N1  UNL     1       0.642   1.315  -0.200  1.00  0.00           N  
HETATM    5  C3  UNL     1       1.987   1.235  -0.034  1.00  0.00           C  
HETATM    6  C4  UNL     1       2.565   0.042   0.277  1.00  0.00           C  
HETATM    7  N2  UNL     1       1.795  -1.057   0.419  1.00  0.00           N  
HETATM    8  C5  UNL     1       0.446  -0.953   0.248  1.00  0.00           C  
HETATM    9  C6  UNL     1      -0.386  -2.167   0.407  1.00  0.00           C  
HETATM   10  H1  UNL     1      -2.925   1.261  -1.443  1.00  0.00           H  
HETATM   11  H2  UNL     1      -1.639   2.271  -0.621  1.00  0.00           H  
HETATM   12  H3  UNL     1      -2.972   1.566   0.345  1.00  0.00           H  
HETATM   13  H4  UNL     1       2.630   2.100  -0.142  1.00  0.00           H  
HETATM   14  H5  UNL     1       3.628  -0.055   0.415  1.00  0.00           H  
HETATM   15  H6  UNL     1       0.103  -2.957   1.005  1.00  0.00           H  
HETATM   16  H7  UNL     1      -1.340  -1.906   0.903  1.00  0.00           H  
HETATM   17  H8  UNL     1      -0.562  -2.569  -0.630  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3
CONECT    3    4    4    8
CONECT    4    5
CONECT    5    6    6   13
CONECT    6    7   14
CONECT    7    8    8
CONECT    8    9
CONECT    9   15   16   17
END
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SMILES for HMDB0031852 (2-Methoxy-3-methylpyrazine)

COC1=NC=CN=C1C
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INCHI for HMDB0031852 (2-Methoxy-3-methylpyrazine)

InChI=1S/C6H8N2O/c1-5-6(9-2)8-4-3-7-5/h3-4H,1-2H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
MethoxymethylpyrazineHMDB
Pyrazine, 2-methyl-3-methoxyHMDB
Chemical FormulaC6H8N2O
Average Molecular Weight124.1405
Monoisotopic Molecular Weight124.063662888
IUPAC Name2-methoxy-3-methylpyrazine
Traditional Namepyrazine, 2-methoxy-3-methyl-
CAS Registry NumberNot Available
SMILES
COC1=NC=CN=C1C
InChI Identifier
InChI=1S/C6H8N2O/c1-5-6(9-2)8-4-3-7-5/h3-4H,1-2H3
InChI KeyVKJIAEQRKBQLLA-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as methoxypyrazines. These are pyrazines containing a methoxyl group attached to the pyrazine ring.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrazines
Direct ParentMethoxypyrazines
Alternative Parents
Substituents
  • Methoxypyrazine
  • Alkyl aryl ether
  • Heteroaromatic compound
  • Azacycle
  • Ether
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Industrial application
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP1.24Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility213 g/LALOGPS
logP1.09ALOGPS
logP0.11ChemAxon
logS0.24ALOGPS
pKa (Strongest Basic)1.21ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area35.01 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity33.11 m³·mol⁻¹ChemAxon
Polarizability12.58 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
DarkChem[M+H]+124.21731661259
DarkChem[M-H]-122.45931661259
DeepCCS[M+H]+126.50230932474
DeepCCS[M-H]-123.13130932474
DeepCCS[M-2H]-160.10730932474
DeepCCS[M+Na]+135.11630932474
AllCCS[M+H]+126.532859911
AllCCS[M+H-H2O]+121.832859911
AllCCS[M+NH4]+131.032859911
AllCCS[M+Na]+132.332859911
AllCCS[M-H]-124.532859911
AllCCS[M+Na-2H]-126.732859911
AllCCS[M+HCOO]-129.232859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.1.84 minutes32390414
Predicted by Siyang on May 30, 20228.9221 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.52 minutes32390414

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-Methoxy-3-methylpyrazineCOC1=C(C)N=CC=N11314.4Standard polar33892256
2-Methoxy-3-methylpyrazineCOC1=C(C)N=CC=N1938.1Standard non polar33892256
2-Methoxy-3-methylpyrazineCOC1=C(C)N=CC=N11000.0Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2-Methoxy-3-methylpyrazine GC-MS (Non-derivatized) - 70eV, Positivesplash10-00dl-9500000000-34dec9f00a47cd6adbc72017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Methoxy-3-methylpyrazine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Methoxy-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-Methoxy-3-methylpyrazine 10V, Positive-QTOFsplash10-004i-0900000000-aad109e07d5cf94af3cb2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-3-methylpyrazine 20V, Positive-QTOFsplash10-004i-1900000000-bac0a547b92218f9e4b82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-3-methylpyrazine 40V, Positive-QTOFsplash10-0k96-9000000000-539c30af84a7bf2d10b02016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-3-methylpyrazine 10V, Negative-QTOFsplash10-00di-0900000000-1e088bb054380e2a4f5b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-3-methylpyrazine 20V, Negative-QTOFsplash10-0a4i-9200000000-ddf5a78cfd9b307ca8f62016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-3-methylpyrazine 40V, Negative-QTOFsplash10-0a6r-9000000000-01df35c8d916c19f85ed2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-3-methylpyrazine 10V, Positive-QTOFsplash10-004i-0900000000-91e201add7488b50382a2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-3-methylpyrazine 20V, Positive-QTOFsplash10-004l-9500000000-221a0f6d956c28a372122021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-3-methylpyrazine 40V, Positive-QTOFsplash10-0f6x-9000000000-503a43cbf499ac3566ed2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-3-methylpyrazine 10V, Negative-QTOFsplash10-00di-1900000000-9a311fbd9156db5eb0a42021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-3-methylpyrazine 20V, Negative-QTOFsplash10-00dl-9800000000-f74af4faf3ef91d117df2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-3-methylpyrazine 40V, Negative-QTOFsplash10-0k96-9000000000-2a12c08e10de41fbf96e2021-09-25Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-04FELIX labView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB008536
KNApSAcK IDNot Available
Chemspider ID16906
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound17898
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. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .