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Showing metabocard for 2,5-Dimethylpyrazine (HMDB0035289)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-11 20:14:46 UTC
Update Date2023-02-21 17:24:45 UTC
HMDB IDHMDB0035289
Secondary Accession Numbers
  • HMDB35289
Metabolite Identification
Common Name2,5-Dimethylpyrazine
Description2,5-Dimethylpyrazine, also known as fema 3272 or pyrazine,2,5-dimethyl, 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. 2,5-Dimethylpyrazine is a cocoa, grass, and medicinal tasting compound. 2,5-Dimethylpyrazine is found, on average, in the highest concentration within kohlrabis. 2,5-Dimethylpyrazine has also been detected, but not quantified, in several different foods, such as green vegetables, soy beans, asparagus, tortilla chips, and fenugreeks. This could make 2,5-dimethylpyrazine a potential biomarker for the consumption of these foods. It occurs naturally in baked potato, black or green tea, crispbread, French fries, malt, peated malt, raw asparagus, roasted barley, roasted filberts or pecans, squid, wheat bread, wild rice (Zizania aquatica), and wort. Alkylpyrazines are chemical compounds based on pyrazine with different substitution patterns. Some alkylpyrazines are naturally occurring highly aromatic substances which often have a very low odor threshold and contribute to the taste and aroma of various foods including coffee and wines. Alkylpyrazines are also formed during the cooking of some foods via Maillard reactions.
Structure
Data?1677000285
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0035289 (2,5-Dimethylpyrazine)


  Mrv1652303202019002D          

  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 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
  5  1  1  0  0  0  0
  5  3  2  0  0  0  0
  6  2  1  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
M  END
Download

3D MOL for HMDB0035289 (2,5-Dimethylpyrazine)

HMDB0035289
     RDKit          3D
2,5-Dimethylpyrazine
 16 16  0  0  0  0  0  0  0  0999 V2000
   -2.8767   -0.0356    0.1948 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3814   -0.0202    0.0996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7038    1.0452   -0.4543 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6502    1.0652   -0.5434 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3772    0.0299   -0.0865 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8646    0.0325   -0.1750 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7009   -1.0344    0.4668 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6544   -1.0547    0.5562 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3009   -0.4841   -0.7375 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1406   -0.7304    1.0151 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2632    0.9759    0.3926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3117    1.8652   -0.8143 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1561    0.4600   -1.1797 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2870   -0.9782   -0.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3123    0.7224    0.5839 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2844   -1.8586    0.8303 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
  8  2  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  3 12  1  0
  6 13  1  0
  6 14  1  0
  6 15  1  0
  7 16  1  0
M  END
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3D SDF for HMDB0035289 (2,5-Dimethylpyrazine)


  Mrv1652303202019002D          

  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 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
  5  1  1  0  0  0  0
  5  3  2  0  0  0  0
  6  2  1  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
M  END
> <DATABASE_ID>
HMDB0035289

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H8N2/c1-5-3-8-6(2)4-7-5/h3-4H,1-2H3

> <INCHI_KEY>
LCZUOKDVTBMCMX-UHFFFAOYSA-N

> <FORMULA>
C6H8N2

> <MOLECULAR_WEIGHT>
108.1411

> <EXACT_MASS>
108.068748266

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
11.91272955330324

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,5-dimethylpyrazine

> <ALOGPS_LOGP>
0.62

> <JCHEM_LOGP>
-0.19935869999999986

> <ALOGPS_LOGS>
0.23

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
1.5864940624182493

> <JCHEM_POLAR_SURFACE_AREA>
25.78

> <JCHEM_REFRACTIVITY>
30.9272

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.84e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,5-dimethylpyrazine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0035289 (2,5-Dimethylpyrazine)

HMDB0035289
     RDKit          3D
2,5-Dimethylpyrazine
 16 16  0  0  0  0  0  0  0  0999 V2000
   -2.8767   -0.0356    0.1948 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3814   -0.0202    0.0996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7038    1.0452   -0.4543 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6502    1.0652   -0.5434 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3772    0.0299   -0.0865 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8646    0.0325   -0.1750 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7009   -1.0344    0.4668 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6544   -1.0547    0.5562 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3009   -0.4841   -0.7375 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1406   -0.7304    1.0151 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2632    0.9759    0.3926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3117    1.8652   -0.8143 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1561    0.4600   -1.1797 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2870   -0.9782   -0.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3123    0.7224    0.5839 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2844   -1.8586    0.8303 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
  8  2  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  3 12  1  0
  6 13  1  0
  6 14  1  0
  6 15  1  0
  7 16  1  0
M  END
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PDB for HMDB0035289 (2,5-Dimethylpyrazine)

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       1.334   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  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
CONECT    1    5                                                            
CONECT    2    6                                                            
CONECT    3    5    8                                                       
CONECT    4    6    7                                                       
CONECT    5    1    3    7                                                  
CONECT    6    2    4    8                                                  
CONECT    7    4    5                                                       
CONECT    8    3    6                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0035289 (2,5-Dimethylpyrazine)

COMPND    HMDB0035289
HETATM    1  C1  UNL     1      -2.877  -0.036   0.195  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.381  -0.020   0.100  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.704   1.045  -0.454  1.00  0.00           C  
HETATM    4  N1  UNL     1       0.650   1.065  -0.543  1.00  0.00           N  
HETATM    5  C4  UNL     1       1.377   0.030  -0.086  1.00  0.00           C  
HETATM    6  C5  UNL     1       2.865   0.032  -0.175  1.00  0.00           C  
HETATM    7  C6  UNL     1       0.701  -1.034   0.467  1.00  0.00           C  
HETATM    8  N2  UNL     1      -0.654  -1.055   0.556  1.00  0.00           N  
HETATM    9  H1  UNL     1      -3.301  -0.484  -0.737  1.00  0.00           H  
HETATM   10  H2  UNL     1      -3.141  -0.730   1.015  1.00  0.00           H  
HETATM   11  H3  UNL     1      -3.263   0.976   0.393  1.00  0.00           H  
HETATM   12  H4  UNL     1      -1.312   1.865  -0.814  1.00  0.00           H  
HETATM   13  H5  UNL     1       3.156   0.460  -1.180  1.00  0.00           H  
HETATM   14  H6  UNL     1       3.287  -0.978  -0.149  1.00  0.00           H  
HETATM   15  H7  UNL     1       3.312   0.722   0.584  1.00  0.00           H  
HETATM   16  H8  UNL     1       1.284  -1.859   0.830  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3    3    8
CONECT    3    4   12
CONECT    4    5    5
CONECT    5    6    7
CONECT    6   13   14   15
CONECT    7    8    8   16
END
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SMILES for HMDB0035289 (2,5-Dimethylpyrazine)

CC1=CN=C(C)C=N1
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INCHI for HMDB0035289 (2,5-Dimethylpyrazine)

InChI=1S/C6H8N2/c1-5-3-8-6(2)4-7-5/h3-4H,1-2H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
25-Dimethyl-pyrazineChEMBL, HMDB
2, 5-DimethylpyrazineHMDB
2,5-Dimethyl pyrazineHMDB
2,5-Dimethyl-1,4-diazineHMDB
2,5-Dimethyl-pyrazineHMDB
2,5-DimethylparadiazineHMDB
2,5-DimethylpiazineHMDB
FEMA 3272HMDB
PYRAZINE,2,5-dimethylHMDB
2,6-DimethylpyrazineMeSH
2,5-DMPMeSH
Chemical FormulaC6H8N2
Average Molecular Weight108.1411
Monoisotopic Molecular Weight108.068748266
IUPAC Name2,5-dimethylpyrazine
Traditional Name2,5-dimethylpyrazine
CAS Registry Number123-32-0
SMILES
CC1=CN=C(C)C=N1
InChI Identifier
InChI=1S/C6H8N2/c1-5-3-8-6(2)4-7-5/h3-4H,1-2H3
InChI KeyLCZUOKDVTBMCMX-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
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot Available
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point15 °CNot Available
Boiling Point154.00 to 156.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility31970 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP0.63Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility184 g/LALOGPS
logP0.62ALOGPS
logP-0.2ChemAxon
logS0.23ALOGPS
pKa (Strongest Basic)1.59ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area25.78 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity30.93 m³·mol⁻¹ChemAxon
Polarizability11.91 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]+121.64631661259
DarkChem[M-H]-118.97531661259
DeepCCS[M+H]+124.93930932474
DeepCCS[M-H]-121.83830932474
DeepCCS[M-2H]-158.60430932474
DeepCCS[M+Na]+133.54830932474
AllCCS[M+H]+121.632859911
AllCCS[M+H-H2O]+116.732859911
AllCCS[M+NH4]+126.232859911
AllCCS[M+Na]+127.632859911
AllCCS[M-H]-122.632859911
AllCCS[M+Na-2H]-125.332859911
AllCCS[M+HCOO]-128.332859911

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. 1.86 minutes32390414
Predicted by Siyang on May 30, 20228.3613 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.07 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid95.6 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid477.1 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid318.4 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid96.8 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid210.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid55.4 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid272.3 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid283.3 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)139.2 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid612.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid34.1 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid800.7 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid202.6 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid230.1 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate532.0 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA417.0 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water309.5 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2,5-DimethylpyrazineCC1=CN=C(C)C=N11305.1Standard polar33892256
2,5-DimethylpyrazineCC1=CN=C(C)C=N1873.1Standard non polar33892256
2,5-DimethylpyrazineCC1=CN=C(C)C=N1920.3Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen Locations
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Campylobacter jejuni infection		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Clostridium difficile infection		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Ulcerative Colitis		 details
Associated Disorders and Diseases
Disease References
Ulcerative colitis
  1. Garner CE, Smith S, de Lacy Costello B, White P, Spencer R, Probert CS, Ratcliffe NM: Volatile organic compounds from feces and their potential for diagnosis of gastrointestinal disease. FASEB J. 2007 Jun;21(8):1675-88. Epub 2007 Feb 21. [PubMed:17314143 ]
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB013954
KNApSAcK IDC00052608
Chemspider ID28992
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkAlkylpyrazine
METLIN IDNot Available
PubChem Compound31252
PDB ID25R
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1008141
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.. .