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Showing metabocard for 2-Methoxy-5-methylpyrazine (HMDB0040141)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 01:41:13 UTC
Update Date2023-02-21 17:27:44 UTC
HMDB IDHMDB0040141
Secondary Accession Numbers
  • HMDB40141
Metabolite Identification
Common Name2-Methoxy-5-methylpyrazine
Description2-Methoxy-5-methylpyrazine belongs to the class of organic compounds known as methoxypyrazines. These are pyrazines containing a methoxyl group attached to the pyrazine ring. Based on a literature review very few articles have been published on 2-Methoxy-5-methylpyrazine.
Structure
Data?1677000464
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0040141 (2-Methoxy-5-methylpyrazine)


  Mrv0541 05061311392D          

  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
    1.4289   -1.6500    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
    0.0000    0.0000    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
    0.7145   -0.4125    0.0000 C   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
    1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  0  0  0  0
  5  3  2  0  0  0  0
  6  4  1  0  0  0  0
  7  4  2  0  0  0  0
  7  5  1  0  0  0  0
  8  3  1  0  0  0  0
  8  6  2  0  0  0  0
  9  2  1  0  0  0  0
  9  6  1  0  0  0  0
M  END
Download

3D MOL for HMDB0040141 (2-Methoxy-5-methylpyrazine)

HMDB0040141
     RDKit          3D
2-Methoxy-5-methylpyrazine
 17 17  0  0  0  0  0  0  0  0999 V2000
    3.2313    0.4747   -0.7220 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4026   -0.6689   -0.6255 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0318   -0.4866   -0.4625 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2037   -1.6054   -0.3660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1144   -1.3965   -0.2093 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6419   -0.1586   -0.1447 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1040    0.0545    0.0291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8098    0.9447   -0.2417 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4948    0.7454   -0.3969 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1416    0.9954    0.2773 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2634    0.2231   -0.9562 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7530    1.1421   -1.4809 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6631   -2.5784   -0.4221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4539    0.6247   -0.8346 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6103   -0.9247    0.1628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2709    0.6577    0.9516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1802    1.9567   -0.1962 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
  6  8  1  0
  8  9  2  0
  9  3  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  4 13  1  0
  7 14  1  0
  7 15  1  0
  7 16  1  0
  8 17  1  0
M  END
Download

3D SDF for HMDB0040141 (2-Methoxy-5-methylpyrazine)


  Mrv0541 05061311392D          

  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
    1.4289   -1.6500    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
    0.0000    0.0000    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
    0.7145   -0.4125    0.0000 C   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
    1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  0  0  0  0
  5  3  2  0  0  0  0
  6  4  1  0  0  0  0
  7  4  2  0  0  0  0
  7  5  1  0  0  0  0
  8  3  1  0  0  0  0
  8  6  2  0  0  0  0
  9  2  1  0  0  0  0
  9  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0040141

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=NC=C(C)N=C1

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

> <INCHI_KEY>
OHQNWZNVCSEVEQ-UHFFFAOYSA-N

> <FORMULA>
C6H8N2O

> <MOLECULAR_WEIGHT>
124.1405

> <EXACT_MASS>
124.063662888

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
12.748961002731274

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-methoxy-5-methylpyrazine

> <ALOGPS_LOGP>
1.11

> <JCHEM_LOGP>
0.10605739533333315

> <ALOGPS_LOGS>
0.30

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
0.8748421998811922

> <JCHEM_POLAR_SURFACE_AREA>
35.010000000000005

> <JCHEM_REFRACTIVITY>
33.112399999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.46e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-methoxy-5-methylpyrazine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0040141 (2-Methoxy-5-methylpyrazine)

HMDB0040141
     RDKit          3D
2-Methoxy-5-methylpyrazine
 17 17  0  0  0  0  0  0  0  0999 V2000
    3.2313    0.4747   -0.7220 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4026   -0.6689   -0.6255 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0318   -0.4866   -0.4625 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2037   -1.6054   -0.3660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1144   -1.3965   -0.2093 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6419   -0.1586   -0.1447 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1040    0.0545    0.0291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8098    0.9447   -0.2417 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4948    0.7454   -0.3969 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1416    0.9954    0.2773 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2634    0.2231   -0.9562 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7530    1.1421   -1.4809 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6631   -2.5784   -0.4221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4539    0.6247   -0.8346 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6103   -0.9247    0.1628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2709    0.6577    0.9516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1802    1.9567   -0.1962 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
  6  8  1  0
  8  9  2  0
  9  3  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  4 13  1  0
  7 14  1  0
  7 15  1  0
  7 16  1  0
  8 17  1  0
M  END
Download

PDB for HMDB0040141 (2-Methoxy-5-methylpyrazine)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667  -3.080   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  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0       2.667   0.000   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
CONECT    1    5                                                            
CONECT    2    9                                                            
CONECT    3    5    8                                                       
CONECT    4    6    7                                                       
CONECT    5    1    3    7                                                  
CONECT    6    4    8    9                                                  
CONECT    7    4    5                                                       
CONECT    8    3    6                                                       
CONECT    9    2    6                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
Download

3D PDB for HMDB0040141 (2-Methoxy-5-methylpyrazine)

COMPND    HMDB0040141
HETATM    1  C1  UNL     1       3.231   0.475  -0.722  1.00  0.00           C  
HETATM    2  O1  UNL     1       2.403  -0.669  -0.625  1.00  0.00           O  
HETATM    3  C2  UNL     1       1.032  -0.487  -0.463  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.204  -1.605  -0.366  1.00  0.00           C  
HETATM    5  N1  UNL     1      -1.114  -1.397  -0.209  1.00  0.00           N  
HETATM    6  C4  UNL     1      -1.642  -0.159  -0.145  1.00  0.00           C  
HETATM    7  C5  UNL     1      -3.104   0.054   0.029  1.00  0.00           C  
HETATM    8  C6  UNL     1      -0.810   0.945  -0.242  1.00  0.00           C  
HETATM    9  N2  UNL     1       0.495   0.745  -0.397  1.00  0.00           N  
HETATM   10  H1  UNL     1       3.142   0.995   0.277  1.00  0.00           H  
HETATM   11  H2  UNL     1       4.263   0.223  -0.956  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.753   1.142  -1.481  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.663  -2.578  -0.422  1.00  0.00           H  
HETATM   14  H5  UNL     1      -3.454   0.625  -0.835  1.00  0.00           H  
HETATM   15  H6  UNL     1      -3.610  -0.925   0.163  1.00  0.00           H  
HETATM   16  H7  UNL     1      -3.271   0.658   0.952  1.00  0.00           H  
HETATM   17  H8  UNL     1      -1.180   1.957  -0.196  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3
CONECT    3    4    4    9
CONECT    4    5   13
CONECT    5    6    6
CONECT    6    7    8
CONECT    7   14   15   16
CONECT    8    9    9   17
END
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SMILES for HMDB0040141 (2-Methoxy-5-methylpyrazine)

COC1=NC=C(C)N=C1
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INCHI for HMDB0040141 (2-Methoxy-5-methylpyrazine)

InChI=1S/C6H8N2O/c1-5-3-8-6(9-2)4-7-5/h3-4H,1-2H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-Methoxy-5-methyl-pyrazineHMDB
6-Methoxy-3-methylpyrazineHMDB
Pyrazine, 2-methyl-5-methoxyHMDB
Chemical FormulaC6H8N2O
Average Molecular Weight124.1405
Monoisotopic Molecular Weight124.063662888
IUPAC Name2-methoxy-5-methylpyrazine
Traditional Name2-methoxy-5-methylpyrazine
CAS Registry Number2882-22-6
SMILES
COC1=NC=C(C)N=C1
InChI Identifier
InChI=1S/C6H8N2O/c1-5-3-8-6(9-2)4-7-5/h3-4H,1-2H3
InChI KeyOHQNWZNVCSEVEQ-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 locationSource
ProcessNot Available
Role
Biological roleIndustrial application
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point167.00 to 168.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility5445 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP1.193 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility246 g/LALOGPS
logP1.11ALOGPS
logP0.11ChemAxon
logS0.3ALOGPS
pKa (Strongest Basic)0.87ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area35.01 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity33.11 m³·mol⁻¹ChemAxon
Polarizability12.75 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]+125.55931661259
DarkChem[M-H]-124.02231661259
DeepCCS[M+H]+128.80630932474
DeepCCS[M-H]-125.18630932474
DeepCCS[M-2H]-162.47930932474
DeepCCS[M+Na]+137.69430932474
AllCCS[M+H]+126.432859911
AllCCS[M+H-H2O]+121.732859911
AllCCS[M+NH4]+130.932859911
AllCCS[M+Na]+132.232859911
AllCCS[M-H]-125.932859911
AllCCS[M+Na-2H]-128.132859911
AllCCS[M+HCOO]-130.632859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-Methoxy-5-methylpyrazineCOC1=NC=C(C)N=C11332.8Standard polar33892256
2-Methoxy-5-methylpyrazineCOC1=NC=C(C)N=C1967.3Standard non polar33892256
2-Methoxy-5-methylpyrazineCOC1=NC=C(C)N=C11010.8Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2-Methoxy-5-methylpyrazine GC-MS (Non-derivatized) - 70eV, Positivesplash10-0fk9-9400000000-7a915bc5c0a87fcbd3bc2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Methoxy-5-methylpyrazine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Methoxy-5-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-5-methylpyrazine 10V, Positive-QTOFsplash10-004i-1900000000-cc6a8c9f456fb56522372017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-5-methylpyrazine 20V, Positive-QTOFsplash10-004i-5900000000-1701ef5afb7e0109cc4e2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-5-methylpyrazine 40V, Positive-QTOFsplash10-0f6x-9000000000-dde4d2cc7634d3c837ea2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-5-methylpyrazine 10V, Negative-QTOFsplash10-00di-2900000000-3e35030d562ee3a6b37f2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-5-methylpyrazine 20V, Negative-QTOFsplash10-0a4i-9000000000-82463ef30ef51b425ed92017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-5-methylpyrazine 40V, Negative-QTOFsplash10-0kdi-9000000000-f2f674fa8fe1b56f45dc2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-5-methylpyrazine 10V, Negative-QTOFsplash10-00di-0900000000-66a6f205907386096d8d2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-5-methylpyrazine 20V, Negative-QTOFsplash10-00xu-9500000000-ab02293d8fecbb6386302021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-5-methylpyrazine 40V, Negative-QTOFsplash10-0f6x-9000000000-c6aeef32b742107535ed2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-5-methylpyrazine 10V, Positive-QTOFsplash10-004i-1900000000-a271d3e7d396bde6d3f32021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-5-methylpyrazine 20V, Positive-QTOFsplash10-004i-9400000000-8c0c686aea7b5da744ec2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methoxy-5-methylpyrazine 40V, Positive-QTOFsplash10-0uxu-9000000000-757c8c7bddc0ebbdcf002021-09-24Wishart 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 IDFDB019838
KNApSAcK IDNot Available
Chemspider ID68637
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound76153
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1464151
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.. .