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Showing NP-Card for 6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine (NP0049508)

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Record Information
Version2.0
Created at2022-03-17 21:13:39 UTC
Updated at2022-03-17 21:13:39 UTC
NP-MRD IDNP0049508
Secondary Accession NumbersNone
Natural Product Identification
Common Name6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine
Description6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine 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. 6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine is a moderately basic compound (based on its pKa). Outside of the human body, 6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine has been detected, but not quantified in, coffee and coffee products. This could make 6,7-dihydro-2,6-dimethyl-5H-cyclopentapyrazine a potential biomarker for the consumption of these foods.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0049508 (6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine)


  Mrv0541 05061311252D          

 11 12  0  0  0  0            999 V2000
   -0.1712    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  0  0  0  0
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  2  1  0  0  0  0
  7  5  1  0  0  0  0
  8  3  1  0  0  0  0
  9  4  1  0  0  0  0
  9  8  2  0  0  0  0
 10  5  2  0  0  0  0
 10  8  1  0  0  0  0
 11  7  2  0  0  0  0
 11  9  1  0  0  0  0
M  END
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3D MOL for NP0049508 (6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine)

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3D SDF for NP0049508 (6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine)

  Mrv0541 05061311252D          

 11 12  0  0  0  0            999 V2000
   -0.1712    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  0  0  0  0
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  2  1  0  0  0  0
  7  5  1  0  0  0  0
  8  3  1  0  0  0  0
  9  4  1  0  0  0  0
  9  8  2  0  0  0  0
 10  5  2  0  0  0  0
 10  8  1  0  0  0  0
 11  7  2  0  0  0  0
 11  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0049508

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1CC2=C(C1)N=C(C)C=N2

> <INCHI_IDENTIFIER>
InChI=1S/C9H12N2/c1-6-3-8-9(4-6)11-7(2)5-10-8/h5-6H,3-4H2,1-2H3

> <INCHI_KEY>
FKMPZHRHBYPYIZ-UHFFFAOYSA-N

> <FORMULA>
C9H12N2

> <MOLECULAR_WEIGHT>
148.205

> <EXACT_MASS>
148.100048394

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
17.12870293900774

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,6-dimethyl-5H,6H,7H-cyclopenta[b]pyrazine

> <ALOGPS_LOGP>
1.75

> <JCHEM_LOGP>
0.7118076916666665

> <ALOGPS_LOGS>
-1.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
1.7697598914177535

> <JCHEM_POLAR_SURFACE_AREA>
25.78

> <JCHEM_REFRACTIVITY>
42.917899999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.12e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,6-dimethyl-5H,6H,7H-cyclopenta[b]pyrazine

> <JCHEM_VEBER_RULE>
1

$$$$

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3D-SDF for NP0049508 (6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine)
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PDB for NP0049508 (6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine)
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      -0.320   2.843   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.591   4.383   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.126   4.089   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       4.924   1.303   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       4.924   4.383   0.000  0.00  0.00           N+0
CONECT    1    6                                                            
CONECT    2    7                                                            
CONECT    3    6    8                                                       
CONECT    4    6    9                                                       
CONECT    5    7   10                                                       
CONECT    6    1    3    4                                                  
CONECT    7    2    5   11                                                  
CONECT    8    3    9   10                                                  
CONECT    9    4    8   11                                                  
CONECT   10    5    8                                                       
CONECT   11    7    9                                                       
MASTER        0    0    0    0    0    0    0    0   11    0   24    0
END

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3D PDB for NP0049508 (6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine)
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SMILES for NP0049508 (6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine)
CC1CC2=C(C1)N=C(C)C=N2
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INCHI for NP0049508 (6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine)
InChI=1S/C9H12N2/c1-6-3-8-9(4-6)11-7(2)5-10-8/h5-6H,3-4H2,1-2H3
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SynonymsNot Available
Chemical FormulaC9H12N2
Average Mass148.2050 Da
Monoisotopic Mass148.10005 Da
IUPAC Name2,6-dimethyl-5H,6H,7H-cyclopenta[b]pyrazine
Traditional Name2,6-dimethyl-5H,6H,7H-cyclopenta[b]pyrazine
CAS Registry Number61928-63-0
SMILES
CC1CC2=C(C1)N=C(C)C=N2
InChI Identifier
InChI=1S/C9H12N2/c1-6-3-8-9(4-6)11-7(2)5-10-8/h5-6H,3-4H2,1-2H3
InChI KeyFKMPZHRHBYPYIZ-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Coffea arabica L.FooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Coffea canephoraFooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
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 heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP1.75ALOGPS
logP0.71ChemAxon
logS-1.1ALOGPS
pKa (Strongest Basic)1.77ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area25.78 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity42.92 m³·mol⁻¹ChemAxon
Polarizability17.13 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0039832  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB019485  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound12306175  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available