Hmdb loader

Showing metabocard for Pyridine-N-oxide (HMDB0256967)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 17:36:22 UTC
Update Date2021-09-26 23:13:00 UTC
HMDB IDHMDB0256967
Secondary Accession NumbersNone
Metabolite Identification
Common NamePyridine-N-oxide
Descriptionpyridine N-oxide, also known as py N-oxide, belongs to the class of organic compounds known as pyridinium derivatives. Pyridinium derivatives are compounds containing a pyridinium ring, which is the cationic form of pyridine. pyridine N-oxide is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on pyridine N-oxide. This compound has been identified in human blood as reported by (PMID: 31557052 ). Pyridine-n-oxide is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Pyridine-N-oxide is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0256967 (Pyridine-N-oxide)


  Mrv0541 05031423232D          

  7  7  0  0  0  0            999 V2000
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    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
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  6  4  2  0  0  0  0
  6  5  1  0  0  0  0
  7  6  2  0  0  0  0
M  END
Download

3D MOL for HMDB0256967 (Pyridine-N-oxide)

HMDB0256967
     RDKit          3D
Pyridine-N-oxide
 12 12  0  0  0  0  0  0  0  0999 V2000
    2.6776   -0.3667    0.0406 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.3156   -0.1808    0.0200 N   0  0  0  0  0  4  0  0  0  0  0  0
    0.5154   -1.2629   -0.0106 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8662   -1.0900   -0.0318 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3919    0.1855   -0.0212 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5443    1.2873    0.0105 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8265    1.0728    0.0309 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8828   -2.2768   -0.0199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5537   -1.9334   -0.0568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4606    0.3524   -0.0371 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9145    2.2843    0.0195 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5132    1.9282    0.0560 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  2  0
  7  2  1  0
  3  8  1  0
  4  9  1  0
  5 10  1  0
  6 11  1  0
  7 12  1  0
M  CHG  2   1  -1   2   1
M  END
Download

3D SDF for HMDB0256967 (Pyridine-N-oxide)


  Mrv0541 05031423232D          

  7  7  0  0  0  0            999 V2000
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    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
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  6  4  2  0  0  0  0
  6  5  1  0  0  0  0
  7  6  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256967

> <DATABASE_NAME>
hmdb

> <SMILES>
O=N1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C5H5NO/c7-6-4-2-1-3-5-6/h1-5H

> <INCHI_KEY>
ILVXOBCQQYKLDS-UHFFFAOYSA-N

> <FORMULA>
C5H5NO

> <MOLECULAR_WEIGHT>
95.0993

> <EXACT_MASS>
95.037113787

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
9.166775211657615

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1λ⁵-pyridin-1-one

> <ALOGPS_LOGP>
-0.88

> <JCHEM_LOGP>
-0.5045835386666667

> <ALOGPS_LOGS>
-0.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
1.0375925176355414

> <JCHEM_POLAR_SURFACE_AREA>
25.46

> <JCHEM_REFRACTIVITY>
27.5906

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.26e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-oxide pyridine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0256967 (Pyridine-N-oxide)

HMDB0256967
     RDKit          3D
Pyridine-N-oxide
 12 12  0  0  0  0  0  0  0  0999 V2000
    2.6776   -0.3667    0.0406 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.3156   -0.1808    0.0200 N   0  0  0  0  0  4  0  0  0  0  0  0
    0.5154   -1.2629   -0.0106 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8662   -1.0900   -0.0318 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3919    0.1855   -0.0212 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5443    1.2873    0.0105 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8265    1.0728    0.0309 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8828   -2.2768   -0.0199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5537   -1.9334   -0.0568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4606    0.3524   -0.0371 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9145    2.2843    0.0195 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5132    1.9282    0.0560 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  2  0
  7  2  1  0
  3  8  1  0
  4  9  1  0
  5 10  1  0
  6 11  1  0
  7 12  1  0
M  CHG  2   1  -1   2   1
M  END
Download

PDB for HMDB0256967 (Pyridine-N-oxide)

HEADER    PROTEIN                                 03-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   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       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    6                                                       
CONECT    6    4    5    7                                                  
CONECT    7    6                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
Download

3D PDB for HMDB0256967 (Pyridine-N-oxide)

COMPND    HMDB0256967
HETATM    1  O1  UNL     1       2.678  -0.367   0.041  1.00  0.00           O1-
HETATM    2  N1  UNL     1       1.316  -0.181   0.020  1.00  0.00           N1+
HETATM    3  C1  UNL     1       0.515  -1.263  -0.011  1.00  0.00           C  
HETATM    4  C2  UNL     1      -0.866  -1.090  -0.032  1.00  0.00           C  
HETATM    5  C3  UNL     1      -1.392   0.185  -0.021  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.544   1.287   0.010  1.00  0.00           C  
HETATM    7  C5  UNL     1       0.826   1.073   0.031  1.00  0.00           C  
HETATM    8  H1  UNL     1       0.883  -2.277  -0.020  1.00  0.00           H  
HETATM    9  H2  UNL     1      -1.554  -1.933  -0.057  1.00  0.00           H  
HETATM   10  H3  UNL     1      -2.461   0.352  -0.037  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.914   2.284   0.020  1.00  0.00           H  
HETATM   12  H5  UNL     1       1.513   1.928   0.056  1.00  0.00           H  
CONECT    1    2
CONECT    2    3    3    7
CONECT    3    4    8
CONECT    4    5    5    9
CONECT    5    6   10
CONECT    6    7    7   11
CONECT    7   12
END
Download

SMILES for HMDB0256967 (Pyridine-N-oxide)

O=N1=CC=CC=C1
Download

INCHI for HMDB0256967 (Pyridine-N-oxide)

InChI=1S/C5H5NO/c7-6-4-2-1-3-5-6/h1-5H
Download
View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
PY N-oxideChEBI
Pyridine oxideChEBI
Pyridine-1-oxideChEBI
Pyridine-N-oxideChEBI
Pyridine N-oxide perchlorateMeSH
Chemical FormulaC5H5NO
Average Molecular Weight95.0993
Monoisotopic Molecular Weight95.037113787
IUPAC Name1λ⁵-pyridin-1-one
Traditional Name1-oxide pyridine
CAS Registry NumberNot Available
SMILES
O=N1=CC=CC=C1
InChI Identifier
InChI=1S/C5H5NO/c7-6-4-2-1-3-5-6/h1-5H
InChI KeyILVXOBCQQYKLDS-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyridinium derivatives. Pyridinium derivatives are compounds containing a pyridinium ring, which is the cationic form of pyridine.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassPyridinium derivatives
Direct ParentPyridinium derivatives
Alternative Parents
Substituents
  • Pyridinium
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
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
logP-0.88ALOGPS
logP-0.5ChemAxon
logS-0.62ALOGPS
pKa (Strongest Basic)1.04ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area25.46 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity27.59 m³·mol⁻¹ChemAxon
Polarizability9.17 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
DeepCCS[M+H]+117.20530932474
DeepCCS[M-H]-114.89930932474
DeepCCS[M-2H]-150.83430932474
DeepCCS[M+Na]+125.57430932474
AllCCS[M+H]+118.432859911
AllCCS[M+H-H2O]+113.132859911
AllCCS[M+NH4]+123.232859911
AllCCS[M+Na]+124.732859911
AllCCS[M-H]-117.232859911
AllCCS[M+Na-2H]-120.232859911
AllCCS[M+HCOO]-123.532859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Pyridine-N-oxideO=N1=CC=CC=C11190.9Standard polar33892256
Pyridine-N-oxideO=N1=CC=CC=C1816.5Standard non polar33892256
Pyridine-N-oxideO=N1=CC=CC=C11102.3Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Pyridine-N-oxide GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9000000000-0c6041e5298b54914fa82021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pyridine-N-oxide GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDC00045533
Chemspider ID12229
KEGG Compound IDNot Available
BioCyc IDCPD0-2087
BiGG IDNot Available
Wikipedia LinkPyridine-N-oxide
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID29136
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 References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]