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Showing metabocard for 2,6-Dimethylpyridine (HMDB0032972)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-11 17:53:01 UTC
Update Date2023-02-21 17:22:53 UTC
HMDB IDHMDB0032972
Secondary Accession Numbers
  • HMDB32972
Metabolite Identification
Common Name2,6-Dimethylpyridine
Description2,6-Dimethylpyridine, also known as alpha,alpha'-lutidine or 2,6-lutidine, 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. 2,6-Dimethylpyridine has been detected, but not quantified in, several different foods, such as black tea, green tea, herbal tea, red tea, and teas (Camellia sinensis). This could make 2,6-dimethylpyridine a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on 2,6-Dimethylpyridine.
Structure
Data?1677000173
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0032972 (2,6-Dimethylpyridine)


  Mrv1652304272018112D          

  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  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  2  0  0  0  0
  6  8  2  0  0  0  0
  7  8  1  0  0  0  0
M  END
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3D MOL for HMDB0032972 (2,6-Dimethylpyridine)

HMDB0032972
     RDKit          3D
2,6-Dimethylpyridine
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.4877   -0.7195    0.4019 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1719   -0.1207    0.0334 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1542    0.9867   -0.7927 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0927    1.4963   -1.0986 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2284    0.8944   -0.5811 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1741   -0.2121    0.2420 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4044   -0.8589    0.7988 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0525   -0.6892    0.5250 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3748   -1.5644    1.0795 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1719    0.0237    0.8532 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9692   -1.0862   -0.5317 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0797    1.4220   -1.1732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1751    2.3670   -1.7440 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2285    1.2706   -0.8022 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2892   -0.6161    0.1900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5671   -0.6129    1.8573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3021   -1.9805    0.7424 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
  6  7  1  0
  6  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
  5 14  1  0
  7 15  1  0
  7 16  1  0
  7 17  1  0
M  END
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3D SDF for HMDB0032972 (2,6-Dimethylpyridine)


  Mrv1652304272018112D          

  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  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  2  0  0  0  0
  6  8  2  0  0  0  0
  7  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0032972

> <DATABASE_NAME>
hmdb

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

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

> <INCHI_KEY>
OISVCGZHLKNMSJ-UHFFFAOYSA-N

> <FORMULA>
C7H9N

> <MOLECULAR_WEIGHT>
107.1531

> <EXACT_MASS>
107.073499293

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
12.541259267724765

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,6-dimethylpyridine

> <ALOGPS_LOGP>
1.60

> <JCHEM_LOGP>
1.0183137269999998

> <ALOGPS_LOGS>
-0.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
6.5430141644626225

> <JCHEM_POLAR_SURFACE_AREA>
12.89

> <JCHEM_REFRACTIVITY>
33.0841

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.83e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
lutidine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0032972 (2,6-Dimethylpyridine)

HMDB0032972
     RDKit          3D
2,6-Dimethylpyridine
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.4877   -0.7195    0.4019 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1719   -0.1207    0.0334 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1542    0.9867   -0.7927 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0927    1.4963   -1.0986 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2284    0.8944   -0.5811 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1741   -0.2121    0.2420 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4044   -0.8589    0.7988 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0525   -0.6892    0.5250 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3748   -1.5644    1.0795 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1719    0.0237    0.8532 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9692   -1.0862   -0.5317 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0797    1.4220   -1.1732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1751    2.3670   -1.7440 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2285    1.2706   -0.8022 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2892   -0.6161    0.1900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5671   -0.6129    1.8573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3021   -1.9805    0.7424 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
  6  7  1  0
  6  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
  5 14  1  0
  7 15  1  0
  7 16  1  0
  7 17  1  0
M  END
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PDB for HMDB0032972 (2,6-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    5                                                       
CONECT    4    3    6                                                       
CONECT    5    3    7                                                       
CONECT    6    1    4    8                                                  
CONECT    7    2    5    8                                                  
CONECT    8    6    7                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0032972 (2,6-Dimethylpyridine)

COMPND    HMDB0032972
HETATM    1  C1  UNL     1       2.488  -0.720   0.402  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.172  -0.121   0.033  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.154   0.987  -0.793  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.093   1.496  -1.099  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.228   0.894  -0.581  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.174  -0.212   0.242  1.00  0.00           C  
HETATM    7  C7  UNL     1      -2.404  -0.859   0.799  1.00  0.00           C  
HETATM    8  N1  UNL     1       0.052  -0.689   0.525  1.00  0.00           N  
HETATM    9  H1  UNL     1       2.375  -1.564   1.079  1.00  0.00           H  
HETATM   10  H2  UNL     1       3.172   0.024   0.853  1.00  0.00           H  
HETATM   11  H3  UNL     1       2.969  -1.086  -0.532  1.00  0.00           H  
HETATM   12  H4  UNL     1       2.080   1.422  -1.173  1.00  0.00           H  
HETATM   13  H5  UNL     1      -0.175   2.367  -1.744  1.00  0.00           H  
HETATM   14  H6  UNL     1      -2.229   1.271  -0.802  1.00  0.00           H  
HETATM   15  H7  UNL     1      -3.289  -0.616   0.190  1.00  0.00           H  
HETATM   16  H8  UNL     1      -2.567  -0.613   1.857  1.00  0.00           H  
HETATM   17  H9  UNL     1      -2.302  -1.980   0.742  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   14
CONECT    6    7    8    8
CONECT    7   15   16   17
END
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SMILES for HMDB0032972 (2,6-Dimethylpyridine)

CC1=CC=CC(C)=N1
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INCHI for HMDB0032972 (2,6-Dimethylpyridine)

InChI=1S/C7H9N/c1-6-4-3-5-7(2)8-6/h3-5H,1-2H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2,6-LutidineChEBI
alpha,Alpha'-dimethylpyridineChEBI
alpha,Alpha'-lutidineChEBI
lutChEBI
LutidineChEBI
a,Alpha'-dimethylpyridineGenerator
Α,alpha'-dimethylpyridineGenerator
a,Alpha'-lutidineGenerator
Α,alpha'-lutidineGenerator
2,6-Dimethyl-pyridineHMDB
2,6-DimethypyridineHMDB
2,6-LutideneHMDB
2,6-Lutidine, 8ciHMDB
alpha,Alpha'-lutidinHMDB
FEMA 3540HMDB
HSDB 79HMDB
Chemical FormulaC7H9N
Average Molecular Weight107.1531
Monoisotopic Molecular Weight107.073499293
IUPAC Name2,6-dimethylpyridine
Traditional Namelutidine
CAS Registry Number108-48-5
SMILES
CC1=CC=CC(C)=N1
InChI Identifier
InChI=1S/C7H9N/c1-6-4-3-5-7(2)8-6/h3-5H,1-2H3
InChI KeyOISVCGZHLKNMSJ-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 Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-6 °CNot Available
Boiling Point143.00 to 145.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility300 mg/mL at 34 °CNot Available
LogP1.68Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility88.3 g/LALOGPS
logP1.6ALOGPS
logP1.02ChemAxon
logS-0.08ALOGPS
pKa (Strongest Basic)6.54ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area12.89 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity33.08 m³·mol⁻¹ChemAxon
Polarizability12.54 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]+121.19431661259
DarkChem[M-H]-118.61531661259
DeepCCS[M+H]+124.15530932474
DeepCCS[M-H]-121.1730932474
DeepCCS[M-2H]-157.75330932474
DeepCCS[M+Na]+132.72630932474
AllCCS[M+H]+116.832859911
AllCCS[M+H-H2O]+111.732859911
AllCCS[M+NH4]+121.632859911
AllCCS[M+Na]+123.032859911
AllCCS[M-H]-120.332859911
AllCCS[M+Na-2H]-122.832859911
AllCCS[M+HCOO]-125.532859911

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. 2.88 minutes32390414
Predicted by Siyang on May 30, 202210.4406 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.88 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid39.8 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1413.3 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid392.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid136.3 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid238.9 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid75.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid304.7 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 Acid284.8 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)124.3 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid807.1 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid165.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid897.9 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid247.2 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid270.6 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate467.6 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA394.9 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water233.4 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2,6-DimethylpyridineCC1=CC=CC(C)=N11258.4Standard polar33892256
2,6-DimethylpyridineCC1=CC=CC(C)=N1875.8Standard non polar33892256
2,6-DimethylpyridineCC1=CC=CC(C)=N1886.7Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen Locations
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
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
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 IDFDB004392
KNApSAcK IDNot Available
Chemspider ID13842613
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link2,6-Lutidine
METLIN IDNot Available
PubChem Compound7937
PDB IDNot Available
ChEBI ID32548
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1005491
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.. .