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Showing metabocard for 2,5-Dimethylpyridine (HMDB0302386)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 17:23:42 UTC
Update Date2021-09-23 17:23:42 UTC
HMDB IDHMDB0302386
Secondary Accession NumbersNone
Metabolite Identification
Common Name2,5-Dimethylpyridine
Description2,5-dimethylpyridine is a member of the class of compounds known as methylpyridines. Methylpyridines are organic compounds containing a pyridine ring substituted at one or more positions by a methyl group. 2,5-dimethylpyridine is soluble (in water) and a very strong basic compound (based on its pKa). 2,5-dimethylpyridine can be found in tea, which makes 2,5-dimethylpyridine a potential biomarker for the consumption of this food product.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0302386 (2,5-Dimethylpyridine)


  Mrv1652304272018152D          

  8  8  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
   -0.8250   -1.4290    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   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  2  7  1  0  0  0  0
  3  4  2  0  0  0  0
  3  6  1  0  0  0  0
  4  7  1  0  0  0  0
  5  6  2  0  0  0  0
  5  8  1  0  0  0  0
  7  8  2  0  0  0  0
M  END
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3D MOL for HMDB0302386 (2,5-Dimethylpyridine)

HMDB0302386
     RDKit          3D
2,5-Dimethylpyridine
 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.8144   -0.0318    0.1747 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3352    0.0015    0.1422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6215   -0.3935   -0.9797 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7649   -0.3590   -1.0013 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4893    0.0695    0.0923 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9781    0.1124    0.0850 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7758    0.4477    1.1692 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5702    0.4230    1.2137 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2420    0.7380    0.8502 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2560    0.1899   -0.8361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2175   -1.0137    0.4679 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2020   -0.7319   -1.8427 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3077   -0.6780   -1.9046 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3751   -0.5416   -0.6910 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3494   -0.1150    1.1025 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3410    1.1449   -0.1485 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1227    0.7377    2.1062 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
  4 13  1  0
  6 14  1  0
  6 15  1  0
  6 16  1  0
  8 17  1  0
M  END
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3D SDF for HMDB0302386 (2,5-Dimethylpyridine)


  Mrv1652304272018152D          

  8  8  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
   -0.8250   -1.4290    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   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  2  7  1  0  0  0  0
  3  4  2  0  0  0  0
  3  6  1  0  0  0  0
  4  7  1  0  0  0  0
  5  6  2  0  0  0  0
  5  8  1  0  0  0  0
  7  8  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0302386

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CN=C(C)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C7H9N/c1-6-3-4-7(2)8-5-6/h3-5H,1-2H3

> <INCHI_KEY>
XWKFPIODWVPXLX-UHFFFAOYSA-N

> <FORMULA>
C7H9N

> <MOLECULAR_WEIGHT>
107.1531

> <EXACT_MASS>
107.073499293

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
12.512193726042849

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,5-dimethylpyridine

> <ALOGPS_LOGP>
1.83

> <JCHEM_LOGP>
1.4003649473333333

> <ALOGPS_LOGS>
-0.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
6.237648948764575

> <JCHEM_POLAR_SURFACE_AREA>
12.89

> <JCHEM_REFRACTIVITY>
33.5338

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.37e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,5-dimethylpyridine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0302386 (2,5-Dimethylpyridine)

HMDB0302386
     RDKit          3D
2,5-Dimethylpyridine
 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.8144   -0.0318    0.1747 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3352    0.0015    0.1422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6215   -0.3935   -0.9797 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7649   -0.3590   -1.0013 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4893    0.0695    0.0923 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9781    0.1124    0.0850 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7758    0.4477    1.1692 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5702    0.4230    1.2137 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2420    0.7380    0.8502 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2560    0.1899   -0.8361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2175   -1.0137    0.4679 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2020   -0.7319   -1.8427 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3077   -0.6780   -1.9046 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3751   -0.5416   -0.6910 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3494   -0.1150    1.1025 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3410    1.1449   -0.1485 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1227    0.7377    2.1062 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
  4 13  1  0
  6 14  1  0
  6 15  1  0
  6 16  1  0
  8 17  1  0
M  END
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PDB for HMDB0302386 (2,5-Dimethylpyridine)

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      -1.540  -2.667   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       0.770   1.334   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      -1.540   0.000   0.000  0.00  0.00           N+0
CONECT    1    6                                                            
CONECT    2    7                                                            
CONECT    3    4    6                                                       
CONECT    4    3    7                                                       
CONECT    5    6    8                                                       
CONECT    6    1    3    5                                                  
CONECT    7    2    4    8                                                  
CONECT    8    5    7                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0302386 (2,5-Dimethylpyridine)

COMPND    HMDB0302386
HETATM    1  C1  UNL     1      -2.814  -0.032   0.175  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.335   0.001   0.142  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.621  -0.394  -0.980  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.765  -0.359  -1.001  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.489   0.070   0.092  1.00  0.00           C  
HETATM    6  C6  UNL     1       2.978   0.112   0.085  1.00  0.00           C  
HETATM    7  N1  UNL     1       0.776   0.448   1.169  1.00  0.00           N  
HETATM    8  C7  UNL     1      -0.570   0.423   1.214  1.00  0.00           C  
HETATM    9  H1  UNL     1      -3.242   0.738   0.850  1.00  0.00           H  
HETATM   10  H2  UNL     1      -3.256   0.190  -0.836  1.00  0.00           H  
HETATM   11  H3  UNL     1      -3.218  -1.014   0.468  1.00  0.00           H  
HETATM   12  H4  UNL     1      -1.202  -0.732  -1.843  1.00  0.00           H  
HETATM   13  H5  UNL     1       1.308  -0.678  -1.905  1.00  0.00           H  
HETATM   14  H6  UNL     1       3.375  -0.542  -0.691  1.00  0.00           H  
HETATM   15  H7  UNL     1       3.349  -0.115   1.102  1.00  0.00           H  
HETATM   16  H8  UNL     1       3.341   1.145  -0.149  1.00  0.00           H  
HETATM   17  H9  UNL     1      -1.123   0.738   2.106  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3    3    8
CONECT    3    4   12
CONECT    4    5    5   13
CONECT    5    6    7
CONECT    6   14   15   16
CONECT    7    8    8
CONECT    8   17
END
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SMILES for HMDB0302386 (2,5-Dimethylpyridine)

CC1=CN=C(C)C=C1
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INCHI for HMDB0302386 (2,5-Dimethylpyridine)

InChI=1S/C7H9N/c1-6-3-4-7(2)8-5-6/h3-5H,1-2H3
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC7H9N
Average Molecular Weight107.1531
Monoisotopic Molecular Weight107.073499293
IUPAC Name2,5-dimethylpyridine
Traditional Name2,5-dimethylpyridine
CAS Registry NumberNot Available
SMILES
CC1=CN=C(C)C=C1
InChI Identifier
InChI=1S/C7H9N/c1-6-3-4-7(2)8-5-6/h3-5H,1-2H3
InChI KeyXWKFPIODWVPXLX-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as methylpyridines. These are organic compounds containing a pyridine ring substituted at one or more positions by a methyl group.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassMethylpyridines
Direct ParentMethylpyridines
Alternative Parents
Substituents
  • Methylpyridine
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateLiquid
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
logP1.83ALOGPS
logP1.4ChemAxon
logS-0.11ALOGPS
pKa (Strongest Basic)6.24ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area12.89 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity33.53 m³·mol⁻¹ChemAxon
Polarizability12.51 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
AllCCS[M+H]+117.50732859911
AllCCS[M+H-H2O]+112.432859911
AllCCS[M+Na]+123.6632859911
AllCCS[M+NH4]+122.2832859911
AllCCS[M-H]-121.63532859911
AllCCS[M+Na-2H]-124.16632859911
AllCCS[M+HCOO]-126.98832859911
DeepCCS[M+H]+124.73830932474
DeepCCS[M-H]-121.36630932474
DeepCCS[M-2H]-158.27130932474
DeepCCS[M+Na]+133.3930932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethylpyridine 10V, Positive-QTOFsplash10-0a4i-0900000000-a8e7062746fe4450a4082016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethylpyridine 20V, Positive-QTOFsplash10-0a4i-4900000000-97aefedf873c0934d4232016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethylpyridine 40V, Positive-QTOFsplash10-1033-9100000000-3c2382c110f3f9830b0d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethylpyridine 10V, Negative-QTOFsplash10-0a4i-0900000000-c6d08600cdd0604586e12016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethylpyridine 20V, Negative-QTOFsplash10-0a4i-0900000000-2bf4d70cc32b4f6e0b752016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethylpyridine 40V, Negative-QTOFsplash10-0a4i-9300000000-8b936c812e84ab517df72016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethylpyridine 10V, Positive-QTOFsplash10-0a4i-1900000000-e6f8c77c38ab3ba6dfa62021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethylpyridine 20V, Positive-QTOFsplash10-0a4i-9700000000-36f489b408b1e4f62f302021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethylpyridine 40V, Positive-QTOFsplash10-0gb9-9000000000-45f493d38c1bea9297482021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethylpyridine 10V, Negative-QTOFsplash10-0a4i-0900000000-95c37ad0f0f4fd79f7e22021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethylpyridine 20V, Negative-QTOFsplash10-0a4i-0900000000-03412eb4108ea6a0e8602021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethylpyridine 40V, Negative-QTOFsplash10-0006-9100000000-43761ad5dcd26736ab782021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
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 IDFDB004388
KNApSAcK IDNot Available
Chemspider ID11042
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
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 ReferencesNot Available