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Showing NP-Card for Azomycin (NP0004765)

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Record Information
Version2.0
Created at2020-12-09 02:11:09 UTC
Updated at2021-07-15 16:50:06 UTC
NP-MRD IDNP0004765
Secondary Accession NumbersNone
Natural Product Identification
Common NameAzomycin
Provided ByNPAtlasNPAtlas Logo
Description2-Nitroimidazole, also known as amicin or azomycin, 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. 2-Nitroimidazole is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Azomycin is found in Pseudomonas fluorescens and Unknown-fungus sp.. It was first documented in 1955 (PMID: 13289298). Based on a literature review a significant number of articles have been published on 2-Nitroimidazole (PMID: 21244596) (PMID: 22710102) (PMID: 22816283) (PMID: 34600326).
Structure
Data?1624574202
MOL3D MOLSDF3D SDFPDBSMILESInChI

MOL for NP0004765 (Azomycin)


  Mrv1652306242118093D          

 11 11  0  0  0  0            999 V2000
   -2.7660    1.0463    0.5247 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0285    0.0583    0.4257 N   0  3  0  0  0  4  0  0  0  0  0  0
   -2.6254   -1.1747    0.3654 O   0  5  0  0  0  1  0  0  0  0  0  0
   -0.6163    0.1976    0.3765 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1325    1.3035    0.4217 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4431    0.9943    0.3458 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5066   -0.3910    0.2475 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2253   -0.8441    0.2696 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3056    1.6459    0.3549 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4201   -0.9710    0.1694 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0029   -1.8652    0.2083 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  4  1  0  0  0  0
  6  9  1  0  0  0  0
  7 10  1  0  0  0  0
  8 11  1  0  0  0  0
M  CHG  2   2   1   3  -1
M  END
Download

3D MOL for NP0004765 (Azomycin)

     RDKit          3D

 11 11  0  0  0  0  0  0  0  0999 V2000
   -2.7660    1.0463    0.5247 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0285    0.0583    0.4257 N   0  0  0  0  0  4  0  0  0  0  0  0
   -2.6254   -1.1747    0.3654 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.6163    0.1976    0.3765 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1325    1.3035    0.4217 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4431    0.9943    0.3458 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5066   -0.3910    0.2475 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2253   -0.8441    0.2696 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3056    1.6459    0.3549 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4201   -0.9710    0.1694 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0029   -1.8652    0.2083 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
  6  9  1  0
  7 10  1  0
  8 11  1  0
M  CHG  2   2   1   3  -1
M  END
Download

3D SDF for NP0004765 (Azomycin)


  Mrv1652306242118093D          

 11 11  0  0  0  0            999 V2000
   -2.7660    1.0463    0.5247 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0285    0.0583    0.4257 N   0  3  0  0  0  4  0  0  0  0  0  0
   -2.6254   -1.1747    0.3654 O   0  5  0  0  0  1  0  0  0  0  0  0
   -0.6163    0.1976    0.3765 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1325    1.3035    0.4217 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4431    0.9943    0.3458 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5066   -0.3910    0.2475 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2253   -0.8441    0.2696 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3056    1.6459    0.3549 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4201   -0.9710    0.1694 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0029   -1.8652    0.2083 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  4  1  0  0  0  0
  6  9  1  0  0  0  0
  7 10  1  0  0  0  0
  8 11  1  0  0  0  0
M  CHG  2   2   1   3  -1
M  END
> <DATABASE_ID>
NP0004765

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]N1C([H])=C([H])N=C1[N+]([O-])=O

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

> <INCHI_KEY>
YZEUHQHUFTYLPH-UHFFFAOYSA-N

> <FORMULA>
C3H3N3O2

> <MOLECULAR_WEIGHT>
113.076

> <EXACT_MASS>
113.022526349

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
11

> <JCHEM_AVERAGE_POLARIZABILITY>
9.224026676749306

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(1H-imidazol-2-yl)nitro]-lambda1-oxidanyl

> <ALOGPS_LOGP>
0.09

> <JCHEM_LOGP>
0.4790099873333334

> <ALOGPS_LOGS>
-0.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.740613866548788

> <JCHEM_PKA_STRONGEST_BASIC>
-1.7316832234024986

> <JCHEM_POLAR_SURFACE_AREA>
71.82

> <JCHEM_REFRACTIVITY>
24.8066

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.75e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1H-imidazol-2-ylnitro)-lambda1-oxidanyl

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0004765 (Azomycin)

     RDKit          3D

 11 11  0  0  0  0  0  0  0  0999 V2000
   -2.7660    1.0463    0.5247 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0285    0.0583    0.4257 N   0  0  0  0  0  4  0  0  0  0  0  0
   -2.6254   -1.1747    0.3654 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.6163    0.1976    0.3765 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1325    1.3035    0.4217 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4431    0.9943    0.3458 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5066   -0.3910    0.2475 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2253   -0.8441    0.2696 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3056    1.6459    0.3549 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4201   -0.9710    0.1694 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0029   -1.8652    0.2083 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
  6  9  1  0
  7 10  1  0
  8 11  1  0
M  CHG  2   2   1   3  -1
M  END
Download

PDB for NP0004765 (Azomycin)

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  O   UNK     0      -2.766   1.046   0.525  0.00  0.00           O+0
HETATM    2  N   UNK     0      -2.029   0.058   0.426  0.00  0.00           N+1
HETATM    3  O   UNK     0      -2.625  -1.175   0.365  0.00  0.00           O-1
HETATM    4  C   UNK     0      -0.616   0.198   0.377  0.00  0.00           C+0
HETATM    5  N   UNK     0       0.133   1.304   0.422  0.00  0.00           N+0
HETATM    6  C   UNK     0       1.443   0.994   0.346  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.507  -0.391   0.248  0.00  0.00           C+0
HETATM    8  N   UNK     0       0.225  -0.844   0.270  0.00  0.00           N+0
HETATM    9  H   UNK     0       2.306   1.646   0.355  0.00  0.00           H+0
HETATM   10  H   UNK     0       2.420  -0.971   0.169  0.00  0.00           H+0
HETATM   11  H   UNK     0       0.003  -1.865   0.208  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    8                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    9                                                  
CONECT    7    6    8   10                                                  
CONECT    8    7    4   11                                                  
CONECT    9    6                                                            
CONECT   10    7                                                            
CONECT   11    8                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
Download

3D PDB for NP0004765 (Azomycin)

Download
SMILES for NP0004765 (Azomycin)
[H]N1C([H])=C([H])N=C1[N+]([O-])=O
Download
INCHI for NP0004765 (Azomycin)
InChI=1S/C3H3N3O2/c7-6(8)3-4-1-2-5-3/h1-2H,(H,4,5)
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View in JSmolView NMR Assignments
Synonyms
ValueSource
AmicinChEBI
AzomycinChEBI
NitroimidazoleChEBI
Azomycin, monohydrofluorideHMDB
Azomycin, sodium saltHMDB
Chemical FormulaC3H3N3O2
Average Mass113.0760 Da
Monoisotopic Mass113.02253 Da
IUPAC Name[(1H-imidazol-2-yl)nitro]-lambda1-oxidanyl
Traditional Name(1H-imidazol-2-ylnitro)-lambda1-oxidanyl
CAS Registry NumberNot Available
SMILES
[O-][N+](=O)C1=NC=CN1
InChI Identifier
InChI=1S/C3H3N3O2/c7-6(8)3-4-1-2-5-3/h1-2H,(H,4,5)
InChI KeyYZEUHQHUFTYLPH-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Pseudomonas fluorescensLOTUS Database
Unknown-fungus sp.NPAtlas
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
    • 

  • Azole
    • 

  • Imidazole
    • 

  • Heteroaromatic compound
    • 

  • Organic oxoazanium
    • 

  • Propargyl-type 1,3-dipolar organic compound
    • 

  • Organoheterocyclic compound
    • 

  • Azacycle
    • 

  • 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
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP0.09ALOGPS
logP0.48ChemAxon
logS-0.61ALOGPS
pKa (Strongest Acidic)7.74ChemAxon
pKa (Strongest Basic)-1.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area71.82 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity24.81 m³·mol⁻¹ChemAxon
Polarizability9.22 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
NPAtlas IDNPA018700  
HMDB IDHMDB0245259  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID10251  
KEGG Compound IDC14531  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNitroimidazole  
METLIN IDNot Available
PubChem Compound10701  
PDB IDNot Available
ChEBI ID67135  
Good Scents IDNot Available
References
General References
  1. NAKAMURA S: Structure of Azomycin, a new antibiotic. Pharm Bull. 1955 Oct;3(5):379-83. doi: 10.1248/cpb1953.3.379. [PubMed:13289298  ] 
  2. Qu Y, Spain JC: Catabolic pathway for 2-nitroimidazole involves a novel nitrohydrolase that also confers drug resistance. Environ Microbiol. 2011 Apr;13(4):1010-7. doi: 10.1111/j.1462-2920.2010.02406.x.  Epub 2011 Jan 18. [PubMed:21244596  ] 
  3. Li Y, Luo Y, Hu Y, Zhu DD, Zhang S, Liu ZJ, Gong HB, Zhu HL: Design, synthesis and antimicrobial activities of nitroimidazole derivatives containing 1,3,4-oxadiazole scaffold as FabH inhibitors. Bioorg Med Chem. 2012 Jul 15;20(14):4316-22. doi: 10.1016/j.bmc.2012.05.050. Epub 2012 May 30. [PubMed:22710102  ] 
  4. Kanda M, Sasamoto T, Takeba K, Hayashi H, Kusano T, Matsushima Y, Nakajima T, Kanai S, Takano I: Rapid determination of nitroimidazole residues in honey by liquid chromatography/tandem mass spectrometry. J AOAC Int. 2012 May-Jun;95(3):923-31. doi: 10.5740/jaoacint.11-362. [PubMed:22816283  ] 
  5. Bera H, Abosheasha MA, Ito Y, Ueda M: Hypoxia-responsive pullulan-based nanoparticles as erlotinib carriers. Int J Biol Macromol. 2021 Sep 29;191:764-774. doi: 10.1016/j.ijbiomac.2021.09.122. [PubMed:34600326  ]