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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
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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

$$$$
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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
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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 locationSource
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 Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20228.9751 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.75 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid953.1 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid359.7 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid106.1 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid262.3 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid74.2 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid292.8 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 Acid307.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)333.2 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid628.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid162.5 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid896.4 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid251.3 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid271.5 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate568.0 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA300.7 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water192.4 seconds40023050

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
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 ]