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Showing metabocard for 2-Nitropyridine (HMDB0245266)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:21:18 UTC
Update Date2021-09-26 22:53:38 UTC
HMDB IDHMDB0245266
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-Nitropyridine
Description2-NITROPYRIDINE belongs to the class of organic compounds known as nitroaromatic compounds. These are c-nitro compounds where the nitro group is C-substituted with an aromatic group. Based on a literature review a significant number of articles have been published on 2-NITROPYRIDINE. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2-nitropyridine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2-Nitropyridine 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0245266 (2-Nitropyridine)


  Mrv1652309112100212D          

  9  9  0  0  0  0            999 V2000
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    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
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    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
    0.7145    2.0625    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
M  CHG  2   7   1   9  -1
M  END
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3D MOL for HMDB0245266 (2-Nitropyridine)

HMDB0245266
     RDKit          3D
2-Nitropyridine
 13 13  0  0  0  0  0  0  0  0999 V2000
    3.0371    0.8422   -0.5599 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3525   -0.1074   -0.1440 N   0  0  0  0  0  4  0  0  0  0  0  0
    2.9706   -1.2644    0.2485 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.9411    0.0524   -0.0940 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1204   -0.9756    0.3625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2473   -0.8084    0.4063 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8507    0.3637    0.0068 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0141    1.3650   -0.4408 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3274    1.1840   -0.4772 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6018   -1.9052    0.6792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8723   -1.6064    0.7598 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9134    0.5543    0.0178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4531    2.3059   -0.7650 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9  4  1  0
  5 10  1  0
  6 11  1  0
  7 12  1  0
  8 13  1  0
M  CHG  2   2   1   3  -1
M  END
Download

3D SDF for HMDB0245266 (2-Nitropyridine)


  Mrv1652309112100212D          

  9  9  0  0  0  0            999 V2000
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    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
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    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
    0.7145    2.0625    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
M  CHG  2   7   1   9  -1
M  END
> <DATABASE_ID>
HMDB0245266

> <DATABASE_NAME>
hmdb

> <SMILES>
[O-][N+](=O)C1=CC=CC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C5H4N2O2/c8-7(9)5-3-1-2-4-6-5/h1-4H

> <INCHI_KEY>
HLTDBMHJSBSAOM-UHFFFAOYSA-N

> <FORMULA>
C5H4N2O2

> <MOLECULAR_WEIGHT>
124.099

> <EXACT_MASS>
124.027277377

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
10.680131700727518

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-nitropyridine

> <ALOGPS_LOGP>
0.96

> <JCHEM_LOGP>
1.2900151083333333

> <ALOGPS_LOGS>
-1.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.138728359609414

> <JCHEM_POLAR_SURFACE_AREA>
56.03

> <JCHEM_REFRACTIVITY>
30.535100000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.26e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-nitropyridine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0245266 (2-Nitropyridine)

HMDB0245266
     RDKit          3D
2-Nitropyridine
 13 13  0  0  0  0  0  0  0  0999 V2000
    3.0371    0.8422   -0.5599 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3525   -0.1074   -0.1440 N   0  0  0  0  0  4  0  0  0  0  0  0
    2.9706   -1.2644    0.2485 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.9411    0.0524   -0.0940 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1204   -0.9756    0.3625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2473   -0.8084    0.4063 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8507    0.3637    0.0068 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0141    1.3650   -0.4408 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3274    1.1840   -0.4772 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6018   -1.9052    0.6792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8723   -1.6064    0.7598 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9134    0.5543    0.0178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4531    2.3059   -0.7650 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9  4  1  0
  5 10  1  0
  6 11  1  0
  7 12  1  0
  8 13  1  0
M  CHG  2   2   1   3  -1
M  END
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PDB for HMDB0245266 (2-Nitropyridine)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.770   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  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       1.334   3.850   0.000  0.00  0.00           N+1
HETATM    8  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O-1
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for HMDB0245266 (2-Nitropyridine)

COMPND    HMDB0245266
HETATM    1  O1  UNL     1       3.037   0.842  -0.560  1.00  0.00           O  
HETATM    2  N1  UNL     1       2.352  -0.107  -0.144  1.00  0.00           N1+
HETATM    3  O2  UNL     1       2.971  -1.264   0.248  1.00  0.00           O1-
HETATM    4  C1  UNL     1       0.941   0.052  -0.094  1.00  0.00           C  
HETATM    5  C2  UNL     1       0.120  -0.976   0.363  1.00  0.00           C  
HETATM    6  C3  UNL     1      -1.247  -0.808   0.406  1.00  0.00           C  
HETATM    7  C4  UNL     1      -1.851   0.364   0.007  1.00  0.00           C  
HETATM    8  C5  UNL     1      -1.014   1.365  -0.441  1.00  0.00           C  
HETATM    9  N2  UNL     1       0.327   1.184  -0.477  1.00  0.00           N  
HETATM   10  H1  UNL     1       0.602  -1.905   0.679  1.00  0.00           H  
HETATM   11  H2  UNL     1      -1.872  -1.606   0.760  1.00  0.00           H  
HETATM   12  H3  UNL     1      -2.913   0.554   0.018  1.00  0.00           H  
HETATM   13  H4  UNL     1      -1.453   2.306  -0.765  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    4    5    5    9
CONECT    5    6   10
CONECT    6    7    7   11
CONECT    7    8   12
CONECT    8    9    9   13
END
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SMILES for HMDB0245266 (2-Nitropyridine)

[O-][N+](=O)C1=CC=CC=N1
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INCHI for HMDB0245266 (2-Nitropyridine)

InChI=1S/C5H4N2O2/c8-7(9)5-3-1-2-4-6-5/h1-4H
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View in JSmolView NMR AssignmentsView Stereo Labels
SynonymsNot Available
Chemical FormulaC5H4N2O2
Average Molecular Weight124.099
Monoisotopic Molecular Weight124.027277377
IUPAC Name2-nitropyridine
Traditional Name2-nitropyridine
CAS Registry NumberNot Available
SMILES
[O-][N+](=O)C1=CC=CC=N1
InChI Identifier
InChI=1S/C5H4N2O2/c8-7(9)5-3-1-2-4-6-5/h1-4H
InChI KeyHLTDBMHJSBSAOM-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as nitroaromatic compounds. These are c-nitro compounds where the nitro group is C-substituted with an aromatic group.
KingdomOrganic compounds
Super ClassOrganic 1,3-dipolar compounds
ClassAllyl-type 1,3-dipolar organic compounds
Sub ClassOrganic nitro compounds
Direct ParentNitroaromatic compounds
Alternative Parents
Substituents
  • Nitroaromatic compound
  • Imidolactam
  • Pyridine
  • Heteroaromatic compound
  • Azacycle
  • Organoheterocyclic compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic oxoazanium
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
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
logP0.96ALOGPS
logP1.29ChemAxon
logS-1.2ALOGPS
pKa (Strongest Basic)-4.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area56.03 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity30.54 m³·mol⁻¹ChemAxon
Polarizability10.68 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+106.15330932474
DeepCCS[M-H]-102.28130932474
DeepCCS[M-2H]-139.85230932474
DeepCCS[M+Na]+115.25430932474
AllCCS[M+H]+124.732859911
AllCCS[M+H-H2O]+119.832859911
AllCCS[M+NH4]+129.232859911
AllCCS[M+Na]+130.632859911
AllCCS[M-H]-119.632859911
AllCCS[M+Na-2H]-121.532859911
AllCCS[M+HCOO]-123.732859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-Nitropyridine[O-][N+](=O)C1=CC=CC=N11699.2Standard polar33892256
2-Nitropyridine[O-][N+](=O)C1=CC=CC=N11081.3Standard non polar33892256
2-Nitropyridine[O-][N+](=O)C1=CC=CC=N11123.7Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2-Nitropyridine GC-MS (Non-derivatized) - 70eV, Positivesplash10-0fk9-9200000000-cc9777974caae3654de72021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Nitropyridine 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)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-12Wishart 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 IDNot Available
Chemspider ID25139
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound26998
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 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 ]