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Showing metabocard for 3-Methoxypyridine (HMDB0302400)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 17:29:52 UTC
Update Date2021-09-23 17:29:52 UTC
HMDB IDHMDB0302400
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-Methoxypyridine
Description3-methoxypyridine is a member of the class of compounds known as alkyl aryl ethers. Alkyl aryl ethers are organic compounds containing the alkyl aryl ether functional group with the generic formula R-O-R' , where R is an alkyl group and R' is an aryl group. 3-methoxypyridine is soluble (in water) and a strong basic compound (based on its pKa). 3-methoxypyridine can be found in tea, which makes 3-methoxypyridine a potential biomarker for the consumption of this food product.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0302400 (3-Methoxypyridine)


  Mrv1652304272018212D          

  8  8  0  0  0  0            999 V2000
   -1.6500   -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   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7145    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   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -1.4290    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  3  6  1  0  0  0  0
  4  7  2  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
M  END
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3D MOL for HMDB0302400 (3-Methoxypyridine)

HMDB0302400
     RDKit          3D
3-Methoxypyridine
 15 15  0  0  0  0  0  0  0  0999 V2000
    2.5493    0.3219   -0.1154 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5650   -0.5259    0.3655 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2101   -0.3803    0.2381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3919    0.6921   -0.4246 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7628    0.7147   -0.4785 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5120   -0.2898    0.1035 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9380   -1.3235    0.7422 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5980   -1.3536    0.7997 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9675   -0.1423   -1.0556 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3811    0.3393    0.6444 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2371    1.3567   -0.3085 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2466    1.4282   -0.8486 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2294    1.5627   -1.0023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5944   -0.1985    0.0168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1303   -2.2016    1.3234 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
  7  8  2  0
  8  3  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  4 12  1  0
  5 13  1  0
  6 14  1  0
  8 15  1  0
M  END
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3D SDF for HMDB0302400 (3-Methoxypyridine)


  Mrv1652304272018212D          

  8  8  0  0  0  0            999 V2000
   -1.6500   -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   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7145    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   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -1.4290    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  3  6  1  0  0  0  0
  4  7  2  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0302400

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=CN=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C6H7NO/c1-8-6-3-2-4-7-5-6/h2-5H,1H3

> <INCHI_KEY>
UMJSCPRVCHMLSP-UHFFFAOYSA-N

> <FORMULA>
C6H7NO

> <MOLECULAR_WEIGHT>
109.1259

> <EXACT_MASS>
109.052763851

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
11.141135746895564

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-methoxypyridine

> <ALOGPS_LOGP>
0.89

> <JCHEM_LOGP>
0.5979021233333335

> <ALOGPS_LOGS>
0.48

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
4.809281224861936

> <JCHEM_POLAR_SURFACE_AREA>
22.12

> <JCHEM_REFRACTIVITY>
30.364299999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.27e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-methyoxypyridine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0302400 (3-Methoxypyridine)

HMDB0302400
     RDKit          3D
3-Methoxypyridine
 15 15  0  0  0  0  0  0  0  0999 V2000
    2.5493    0.3219   -0.1154 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5650   -0.5259    0.3655 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2101   -0.3803    0.2381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3919    0.6921   -0.4246 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7628    0.7147   -0.4785 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5120   -0.2898    0.1035 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9380   -1.3235    0.7422 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5980   -1.3536    0.7997 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9675   -0.1423   -1.0556 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3811    0.3393    0.6444 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2371    1.3567   -0.3085 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2466    1.4282   -0.8486 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2294    1.5627   -1.0023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5944   -0.1985    0.0168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1303   -2.2016    1.3234 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
  7  8  2  0
  8  3  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  4 12  1  0
  5 13  1  0
  6 14  1  0
  8 15  1  0
M  END
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PDB for HMDB0302400 (3-Methoxypyridine)

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      -3.080  -2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.770  -1.334   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      -1.540   0.000   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  N   UNK     0      -0.770   1.334   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0      -1.540  -2.667   0.000  0.00  0.00           O+0
CONECT    1    8                                                            
CONECT    2    3    4                                                       
CONECT    3    2    6                                                       
CONECT    4    2    7                                                       
CONECT    5    6    7                                                       
CONECT    6    3    5    8                                                  
CONECT    7    4    5                                                       
CONECT    8    1    6                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0302400 (3-Methoxypyridine)

COMPND    HMDB0302400
HETATM    1  C1  UNL     1       2.549   0.322  -0.115  1.00  0.00           C  
HETATM    2  O1  UNL     1       1.565  -0.526   0.365  1.00  0.00           O  
HETATM    3  C2  UNL     1       0.210  -0.380   0.238  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.392   0.692  -0.425  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.763   0.715  -0.479  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.512  -0.290   0.104  1.00  0.00           C  
HETATM    7  N1  UNL     1      -1.938  -1.324   0.742  1.00  0.00           N  
HETATM    8  C6  UNL     1      -0.598  -1.354   0.800  1.00  0.00           C  
HETATM    9  H1  UNL     1       2.967  -0.142  -1.056  1.00  0.00           H  
HETATM   10  H2  UNL     1       3.381   0.339   0.644  1.00  0.00           H  
HETATM   11  H3  UNL     1       2.237   1.357  -0.309  1.00  0.00           H  
HETATM   12  H4  UNL     1       0.247   1.428  -0.849  1.00  0.00           H  
HETATM   13  H5  UNL     1      -2.229   1.563  -1.002  1.00  0.00           H  
HETATM   14  H6  UNL     1      -3.594  -0.198   0.017  1.00  0.00           H  
HETATM   15  H7  UNL     1      -0.130  -2.202   1.323  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3
CONECT    3    4    4    8
CONECT    4    5   12
CONECT    5    6    6   13
CONECT    6    7   14
CONECT    7    8    8
CONECT    8   15
END
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SMILES for HMDB0302400 (3-Methoxypyridine)

COC1=CN=CC=C1
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INCHI for HMDB0302400 (3-Methoxypyridine)

InChI=1S/C6H7NO/c1-8-6-3-2-4-7-5-6/h2-5H,1H3
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC6H7NO
Average Molecular Weight109.1259
Monoisotopic Molecular Weight109.052763851
IUPAC Name3-methoxypyridine
Traditional Name3-methyoxypyridine
CAS Registry NumberNot Available
SMILES
COC1=CN=CC=C1
InChI Identifier
InChI=1S/C6H7NO/c1-8-6-3-2-4-7-5-6/h2-5H,1H3
InChI KeyUMJSCPRVCHMLSP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alkyl aryl ethers. These are organic compounds containing the alkyl aryl ether functional group with the generic formula R-O-R' , where R is an alkyl group and R' is an aryl group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassEthers
Direct ParentAlkyl aryl ethers
Alternative Parents
Substituents
  • Alkyl aryl ether
  • Pyridine
  • Heteroaromatic compound
  • Azacycle
  • Organoheterocyclic compound
  • 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
StateNot Available
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
logP0.89ALOGPS
logP0.6ChemAxon
logS0.48ALOGPS
pKa (Strongest Basic)4.81ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area22.12 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity30.36 m³·mol⁻¹ChemAxon
Polarizability11.14 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]+120.98532859911
AllCCS[M+H-H2O]+115.92132859911
AllCCS[M+Na]+127.08532859911
AllCCS[M+NH4]+125.71832859911
AllCCS[M-H]-120.89432859911
AllCCS[M+Na-2H]-123.43332859911
AllCCS[M+HCOO]-126.25932859911
DeepCCS[M+H]+123.10430932474
DeepCCS[M-H]-120.42430932474
DeepCCS[M-2H]-156.78730932474
DeepCCS[M+Na]+131.49630932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methoxypyridine 10V, Positive-QTOFsplash10-03di-0900000000-6a41285c8fb75706cea72016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methoxypyridine 20V, Positive-QTOFsplash10-03di-3900000000-ec8a3a1b1f60c81f73d42016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methoxypyridine 40V, Positive-QTOFsplash10-0f89-9000000000-4d60b20e408e044bc6d42016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methoxypyridine 10V, Negative-QTOFsplash10-0a4i-0900000000-38111d7b63faf9823ede2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methoxypyridine 20V, Negative-QTOFsplash10-0a4i-1900000000-5ac616cf32f58077a06b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methoxypyridine 40V, Negative-QTOFsplash10-0pdi-9000000000-2fb177ba618d57c6c1c32016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methoxypyridine 10V, Negative-QTOFsplash10-0a4i-0900000000-875d8abd6f6773a406342021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methoxypyridine 20V, Negative-QTOFsplash10-0a6r-8900000000-876bfa9c1b7d06b677a22021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methoxypyridine 40V, Negative-QTOFsplash10-0udi-9000000000-20b0c32e6021f84575aa2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methoxypyridine 10V, Positive-QTOFsplash10-03di-0900000000-c89e2460dc3caf4abe052021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methoxypyridine 20V, Positive-QTOFsplash10-0f89-9100000000-dfd504accd21516e74e22021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methoxypyridine 40V, Positive-QTOFsplash10-0w5i-9000000000-41968634ac8d49c554e02021-10-21Wishart 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 IDFDB004414
KNApSAcK IDC00050701
Chemspider ID22179
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound23719
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