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Showing metabocard for 4-Nitroimidazole (HMDB0246535)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:33:08 UTC
Update Date2021-09-26 22:55:41 UTC
HMDB IDHMDB0246535
Secondary Accession NumbersNone
Metabolite Identification
Common Name4-Nitroimidazole
Description5-nitroimidazole belongs to the class of organic compounds known as nitroimidazoles. Nitroimidazoles are compounds containing an imidazole ring which bears a nitro group. Based on a literature review a significant number of articles have been published on 5-nitroimidazole. This compound has been identified in human blood as reported by (PMID: 31557052 ). 4-nitroimidazole is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 4-Nitroimidazole 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 HMDB0246535 (4-Nitroimidazole)


  Mrv1652306031608312D          

  8  8  0  0  0  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  1  1  0  0  0  0
  4  2  2  0  0  0  0
  5  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  3  1  0  0  0  0
  7  6  2  0  0  0  0
  8  6  2  0  0  0  0
M  END
Download

3D MOL for HMDB0246535 (4-Nitroimidazole)

HMDB0246535
     RDKit          3D
4-Nitroimidazole
 11 11  0  0  0  0  0  0  0  0999 V2000
   -2.2370   -1.3436   -0.2014 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8038   -0.2012    0.0093 N   0  0  0  0  0  4  0  0  0  0  0  0
   -2.6424    0.8566    0.2379 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.4004    0.0448    0.0195 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2409    1.2470    0.2363 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5592    1.0073    0.1542 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7818   -0.2857   -0.1036 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5749   -0.8663   -0.1842 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2289    2.2218    0.4388 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7467   -0.8024   -0.2302 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4090   -1.8781   -0.3767 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  4  1  0
  5  9  1  0
  7 10  1  0
  8 11  1  0
M  CHG  2   2   1   3  -1
M  END
Download

3D SDF for HMDB0246535 (4-Nitroimidazole)


  Mrv1652306031608312D          

  8  8  0  0  0  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  1  1  0  0  0  0
  4  2  2  0  0  0  0
  5  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  3  1  0  0  0  0
  7  6  2  0  0  0  0
  8  6  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0246535

> <DATABASE_NAME>
hmdb

> <SMILES>
O=N(=O)C1=CN=CN1

> <INCHI_IDENTIFIER>
InChI=1S/C3H3N3O2/c7-6(8)3-1-4-2-5-3/h1-2H,(H,4,5)

> <INCHI_KEY>
VYDWQPKRHOGLPA-UHFFFAOYSA-N

> <FORMULA>
C3H3N3O2

> <MOLECULAR_WEIGHT>
113.076

> <EXACT_MASS>
113.022526349

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
11

> <JCHEM_AVERAGE_POLARIZABILITY>
8.910241186334563

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-nitro-1H-imidazole

> <ALOGPS_LOGP>
-0.04

> <JCHEM_LOGP>
-0.11594900899999981

> <ALOGPS_LOGS>
-0.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.871927169915355

> <JCHEM_PKA_STRONGEST_BASIC>
2.7844230844175293

> <JCHEM_POLAR_SURFACE_AREA>
74.5

> <JCHEM_REFRACTIVITY>
25.5908

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.02e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1H-imidazole, 5-nitro-

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0246535 (4-Nitroimidazole)

HMDB0246535
     RDKit          3D
4-Nitroimidazole
 11 11  0  0  0  0  0  0  0  0999 V2000
   -2.2370   -1.3436   -0.2014 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8038   -0.2012    0.0093 N   0  0  0  0  0  4  0  0  0  0  0  0
   -2.6424    0.8566    0.2379 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.4004    0.0448    0.0195 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2409    1.2470    0.2363 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5592    1.0073    0.1542 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7818   -0.2857   -0.1036 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5749   -0.8663   -0.1842 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2289    2.2218    0.4388 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7467   -0.8024   -0.2302 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4090   -1.8781   -0.3767 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  4  1  0
  5  9  1  0
  7 10  1  0
  8 11  1  0
M  CHG  2   2   1   3  -1
M  END
Download

PDB for HMDB0246535 (4-Nitroimidazole)

HEADER    PROTEIN                                 03-JUN-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-JUN-16         0                                  
HETATM    1  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       1.830  -0.290   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0      -0.186   1.175   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       1.060   3.620   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0      -0.274   4.390   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       2.393   4.390   0.000  0.00  0.00           O+0
CONECT    1    3    4                                                       
CONECT    2    4    5                                                       
CONECT    3    1    5    6                                                  
CONECT    4    1    2                                                       
CONECT    5    2    3                                                       
CONECT    6    3    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0246535 (4-Nitroimidazole)

COMPND    HMDB0246535
HETATM    1  O1  UNL     1      -2.237  -1.344  -0.201  1.00  0.00           O  
HETATM    2  N1  UNL     1      -1.804  -0.201   0.009  1.00  0.00           N1+
HETATM    3  O2  UNL     1      -2.642   0.857   0.238  1.00  0.00           O1-
HETATM    4  C1  UNL     1      -0.400   0.045   0.019  1.00  0.00           C  
HETATM    5  C2  UNL     1       0.241   1.247   0.236  1.00  0.00           C  
HETATM    6  N2  UNL     1       1.559   1.007   0.154  1.00  0.00           N  
HETATM    7  C3  UNL     1       1.782  -0.286  -0.104  1.00  0.00           C  
HETATM    8  N3  UNL     1       0.575  -0.866  -0.184  1.00  0.00           N  
HETATM    9  H1  UNL     1      -0.229   2.222   0.439  1.00  0.00           H  
HETATM   10  H2  UNL     1       2.747  -0.802  -0.230  1.00  0.00           H  
HETATM   11  H3  UNL     1       0.409  -1.878  -0.377  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    4    5    5    8
CONECT    5    6    9
CONECT    6    7    7
CONECT    7    8   10
CONECT    8   11
END
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SMILES for HMDB0246535 (4-Nitroimidazole)

O=N(=O)C1=CN=CN1
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INCHI for HMDB0246535 (4-Nitroimidazole)

InChI=1S/C3H3N3O2/c7-6(8)3-1-4-2-5-3/h1-2H,(H,4,5)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
4-Nitro-3H-imidazoleChEBI
5(4)-NitroimidazoleChEBI
5-NitroimidazoleMeSH
Chemical FormulaC3H3N3O2
Average Molecular Weight113.076
Monoisotopic Molecular Weight113.022526349
IUPAC Name5-nitro-1H-imidazole
Traditional Name1H-imidazole, 5-nitro-
CAS Registry NumberNot Available
SMILES
O=N(=O)C1=CN=CN1
InChI Identifier
InChI=1S/C3H3N3O2/c7-6(8)3-1-4-2-5-3/h1-2H,(H,4,5)
InChI KeyVYDWQPKRHOGLPA-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as nitroimidazoles. Nitroimidazoles are compounds containing an imidazole ring which bears a nitro group.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassAzoles
Sub ClassImidazoles
Direct ParentNitroimidazoles
Alternative Parents
Substituents
  • Nitroaromatic compound
  • Nitroimidazole
  • Heteroaromatic compound
  • C-nitro compound
  • Organic nitro compound
  • Organic oxoazanium
  • Allyl-type 1,3-dipolar organic compound
  • Propargyl-type 1,3-dipolar organic compound
  • Azacycle
  • Organic 1,3-dipolar compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organic zwitterion
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic oxygen 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-0.04ALOGPS
logP-0.12ChemAxon
logS-0.57ALOGPS
pKa (Strongest Acidic)5.87ChemAxon
pKa (Strongest Basic)2.78ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area74.5 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity25.59 m³·mol⁻¹ChemAxon
Polarizability8.91 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]+118.52530932474
DeepCCS[M-H]-116.01130932474
DeepCCS[M-2H]-152.54330932474
DeepCCS[M+Na]+127.41930932474
AllCCS[M+H]+125.232859911
AllCCS[M+H-H2O]+120.432859911
AllCCS[M+NH4]+129.732859911
AllCCS[M+Na]+131.032859911
AllCCS[M-H]-116.432859911
AllCCS[M+Na-2H]-119.032859911
AllCCS[M+HCOO]-121.832859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
4-NitroimidazoleO=N(=O)C1=CN=CN12068.7Standard polar33892256
4-NitroimidazoleO=N(=O)C1=CN=CN11344.9Standard non polar33892256
4-NitroimidazoleO=N(=O)C1=CN=CN11459.0Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
4-Nitroimidazole,1TMS,isomer #1C[Si](C)(C)N1C=NC=C1[N+](=O)[O-]1338.3Semi standard non polar33892256
4-Nitroimidazole,1TMS,isomer #1C[Si](C)(C)N1C=NC=C1[N+](=O)[O-]1350.1Standard non polar33892256
4-Nitroimidazole,1TMS,isomer #1C[Si](C)(C)N1C=NC=C1[N+](=O)[O-]1866.4Standard polar33892256
4-Nitroimidazole,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=NC=C1[N+](=O)[O-]1592.6Semi standard non polar33892256
4-Nitroimidazole,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=NC=C1[N+](=O)[O-]1563.1Standard non polar33892256
4-Nitroimidazole,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=NC=C1[N+](=O)[O-]1952.6Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 4-Nitroimidazole GC-MS (Non-derivatized) - 70eV, Positivesplash10-03fs-9400000000-77eea377f7676797eec22021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 4-Nitroimidazole GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Nitroimidazole 10V, Positive-QTOFsplash10-03di-1900000000-7845b4d9881f548204c02019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Nitroimidazole 20V, Positive-QTOFsplash10-00ks-9100000000-f7c3babb9d06ef7f9d8a2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Nitroimidazole 40V, Positive-QTOFsplash10-0f6w-9000000000-825ebacc9844df6380792019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Nitroimidazole 10V, Negative-QTOFsplash10-03di-0900000000-f72ff4b965c5bce8c5c32019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Nitroimidazole 20V, Negative-QTOFsplash10-03di-0900000000-d2bf27af51075081cfb82019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Nitroimidazole 40V, Negative-QTOFsplash10-01ox-9700000000-3f0ec57ce2bd4227771d2019-02-23Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart 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 ID17197
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNitroimidazole
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID64635
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 ]