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Showing metabocard for 1,3-Dinitrobenzene (HMDB0244170)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 21:21:10 UTC
Update Date2021-09-26 22:51:45 UTC
HMDB IDHMDB0244170
Secondary Accession NumbersNone
Metabolite Identification
Common Name1,3-Dinitrobenzene
Description1,3-Dinitrobenzene, also known as dinitrophenylene or m-DNB, belongs to the class of organic compounds known as nitrobenzenes. Nitrobenzenes are compounds containing a nitrobenzene moiety, which consists of a benzene ring with a carbon bearing a nitro group. Based on a literature review a small amount of articles have been published on 1,3-Dinitrobenzene. This compound has been identified in human blood as reported by (PMID: 31557052 ). 1,3-dinitrobenzene is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 1,3-Dinitrobenzene 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 HMDB0244170 (1,3-Dinitrobenzene)


  Mrv0541 02231216222D          

 12 12  0  0  0  0            999 V2000
   -0.7145   -1.2375    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 O   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 C   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
    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
    0.7145    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  5  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  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  9  2  0  0  0  0
  4  9  1  0  0  0  0
  6 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
M  CHG  4   1  -1   2   1  10   1  11  -1
M  END
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3D MOL for HMDB0244170 (1,3-Dinitrobenzene)

HMDB0244170
     RDKit          3D
1,3-Dinitrobenzene
 16 16  0  0  0  0  0  0  0  0999 V2000
    2.5006   -2.0991   -0.1406 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4650   -0.8734   -0.1167 N   0  0  0  0  0  4  0  0  0  0  0  0
    3.6071   -0.1110   -0.1492 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.2204   -0.1906   -0.0534 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1369    1.1864   -0.0246 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0945    1.8468    0.0378 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2454    1.0885    0.0709 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1900   -0.2942    0.0431 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3782   -1.0671    0.0774 N   0  0  0  0  0  4  0  0  0  0  0  0
   -2.2919   -2.3104    0.0510 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6289   -0.5230    0.1385 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.0438   -0.8991   -0.0184 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0657    1.7291   -0.0525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0898    2.9266    0.0575 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2142    1.5747    0.1194 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0934   -1.9845   -0.0404 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  1  0
  9 10  2  0
  9 11  1  0
  8 12  2  0
 12  4  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  0
 12 16  1  0
M  CHG  4   2   1   3  -1   9   1  11  -1
M  END
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3D SDF for HMDB0244170 (1,3-Dinitrobenzene)


  Mrv0541 02231216222D          

 12 12  0  0  0  0            999 V2000
   -0.7145   -1.2375    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 O   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 C   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
    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
    0.7145    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  5  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  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  9  2  0  0  0  0
  4  9  1  0  0  0  0
  6 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
M  CHG  4   1  -1   2   1  10   1  11  -1
M  END
> <DATABASE_ID>
HMDB0244170

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H4N2O4/c9-7(10)5-2-1-3-6(4-5)8(11)12/h1-4H

> <INCHI_KEY>
WDCYWAQPCXBPJA-UHFFFAOYSA-N

> <FORMULA>
C6H4N2O4

> <MOLECULAR_WEIGHT>
168.107

> <EXACT_MASS>
168.017106626

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
13.592838678788997

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,3-dinitrobenzene

> <ALOGPS_LOGP>
1.70

> <JCHEM_LOGP>
1.8532141946666667

> <ALOGPS_LOGS>
-3.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
91.63999999999999

> <JCHEM_REFRACTIVITY>
40.7074

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.47e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,4-dinitrobenzene

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0244170 (1,3-Dinitrobenzene)

HMDB0244170
     RDKit          3D
1,3-Dinitrobenzene
 16 16  0  0  0  0  0  0  0  0999 V2000
    2.5006   -2.0991   -0.1406 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4650   -0.8734   -0.1167 N   0  0  0  0  0  4  0  0  0  0  0  0
    3.6071   -0.1110   -0.1492 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.2204   -0.1906   -0.0534 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1369    1.1864   -0.0246 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0945    1.8468    0.0378 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2454    1.0885    0.0709 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1900   -0.2942    0.0431 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3782   -1.0671    0.0774 N   0  0  0  0  0  4  0  0  0  0  0  0
   -2.2919   -2.3104    0.0510 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6289   -0.5230    0.1385 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.0438   -0.8991   -0.0184 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0657    1.7291   -0.0525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0898    2.9266    0.0575 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2142    1.5747    0.1194 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0934   -1.9845   -0.0404 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  1  0
  9 10  2  0
  9 11  1  0
  8 12  2  0
 12  4  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  0
 12 16  1  0
M  CHG  4   2   1   3  -1   9   1  11  -1
M  END
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PDB for HMDB0244170 (1,3-Dinitrobenzene)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O-1
HETATM    2  N   UNK     0      -1.334  -0.770   0.000  0.00  0.00           N+1
HETATM    3  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+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   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       1.334   3.850   0.000  0.00  0.00           N+1
HETATM   11  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O-1
HETATM   12  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   10                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    4                                                       
CONECT   10    6   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END
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3D PDB for HMDB0244170 (1,3-Dinitrobenzene)

COMPND    HMDB0244170
HETATM    1  O1  UNL     1       2.501  -2.099  -0.141  1.00  0.00           O  
HETATM    2  N1  UNL     1       2.465  -0.873  -0.117  1.00  0.00           N1+
HETATM    3  O2  UNL     1       3.607  -0.111  -0.149  1.00  0.00           O1-
HETATM    4  C1  UNL     1       1.220  -0.191  -0.053  1.00  0.00           C  
HETATM    5  C2  UNL     1       1.137   1.186  -0.025  1.00  0.00           C  
HETATM    6  C3  UNL     1      -0.094   1.847   0.038  1.00  0.00           C  
HETATM    7  C4  UNL     1      -1.245   1.089   0.071  1.00  0.00           C  
HETATM    8  C5  UNL     1      -1.190  -0.294   0.043  1.00  0.00           C  
HETATM    9  N2  UNL     1      -2.378  -1.067   0.077  1.00  0.00           N1+
HETATM   10  O3  UNL     1      -2.292  -2.310   0.051  1.00  0.00           O  
HETATM   11  O4  UNL     1      -3.629  -0.523   0.139  1.00  0.00           O1-
HETATM   12  C6  UNL     1       0.044  -0.899  -0.018  1.00  0.00           C  
HETATM   13  H1  UNL     1       2.066   1.729  -0.052  1.00  0.00           H  
HETATM   14  H2  UNL     1      -0.090   2.927   0.058  1.00  0.00           H  
HETATM   15  H3  UNL     1      -2.214   1.575   0.119  1.00  0.00           H  
HETATM   16  H4  UNL     1       0.093  -1.984  -0.040  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    4    5    5   12
CONECT    5    6   13
CONECT    6    7    7   14
CONECT    7    8   15
CONECT    8    9   12   12
CONECT    9   10   10   11
CONECT   12   16
END
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SMILES for HMDB0244170 (1,3-Dinitrobenzene)

[O-][N+](=O)C1=CC(=CC=C1)[N+]([O-])=O
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INCHI for HMDB0244170 (1,3-Dinitrobenzene)

InChI=1S/C6H4N2O4/c9-7(10)5-2-1-3-6(4-5)8(11)12/h1-4H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1,3-DinitrobenzolChEBI
2,4-DinitrobenzeneChEBI
DINITROPHENYLENEChEBI
m-DinitrobenzeneChEBI
m-DNBChEBI
Meta-dinitrobenzeneChEBI
3-DinitrobenzeneHMDB
Chemical FormulaC6H4N2O4
Average Molecular Weight168.107
Monoisotopic Molecular Weight168.017106626
IUPAC Name1,3-dinitrobenzene
Traditional Name2,4-dinitrobenzene
CAS Registry NumberNot Available
SMILES
[O-][N+](=O)C1=CC(=CC=C1)[N+]([O-])=O
InChI Identifier
InChI=1S/C6H4N2O4/c9-7(10)5-2-1-3-6(4-5)8(11)12/h1-4H
InChI KeyWDCYWAQPCXBPJA-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as nitrobenzenes. Nitrobenzenes are compounds containing a nitrobenzene moiety, which consists of a benzene ring with a carbon bearing a nitro group.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassNitrobenzenes
Direct ParentNitrobenzenes
Alternative Parents
Substituents
  • Nitrobenzene
  • Nitroaromatic compound
  • Organic nitro compound
  • C-nitro compound
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Allyl-type 1,3-dipolar organic compound
  • Organic oxoazanium
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
ProcessNot Available
Role
Biological role
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
logP1.7ALOGPS
logP1.85ChemAxon
logS-3.1ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area91.64 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity40.71 m³·mol⁻¹ChemAxon
Polarizability13.59 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]+121.99130932474
DeepCCS[M-H]-119.53230932474
DeepCCS[M-2H]-155.16830932474
DeepCCS[M+Na]+130.01630932474
AllCCS[M+H]+132.532859911
AllCCS[M+H-H2O]+128.132859911
AllCCS[M+NH4]+136.632859911
AllCCS[M+Na]+137.832859911
AllCCS[M-H]-124.532859911
AllCCS[M+Na-2H]-125.132859911
AllCCS[M+HCOO]-126.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1,3-Dinitrobenzene[O-][N+](=O)C1=CC(=CC=C1)[N+]([O-])=O2528.2Standard polar33892256
1,3-Dinitrobenzene[O-][N+](=O)C1=CC(=CC=C1)[N+]([O-])=O1355.2Standard non polar33892256
1,3-Dinitrobenzene[O-][N+](=O)C1=CC(=CC=C1)[N+]([O-])=O1433.9Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - 1,3-Dinitrobenzene EI-B (Non-derivatized)splash10-0fb9-9100000000-ce6bfeb5ef2ced4681a22017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - 1,3-Dinitrobenzene EI-B (Non-derivatized)splash10-00pi-9200000000-c1a87d65c320c33184e32017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - 1,3-Dinitrobenzene EI-B (Non-derivatized)splash10-00pi-9200000000-97cd4c3ebec0ccbd0bca2017-09-12HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1,3-Dinitrobenzene GC-MS (Non-derivatized) - 70eV, Positivesplash10-014j-9700000000-f21228ba810672e355692021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1,3-Dinitrobenzene GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
MSMass Spectrum (Electron Ionization)splash10-00pi-9200000000-1fab7ad275aef5be69ad2014-09-20Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - 1,3-Dinitrobenzene APCI-ITFT , negative-QTOFsplash10-000i-0900000000-38869faeae4bd7e732172017-09-14HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dinitrobenzene 10V, Positive-QTOFsplash10-014i-0900000000-8e6e1e3044163af9bb882016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dinitrobenzene 20V, Positive-QTOFsplash10-03xu-0900000000-fc0ea1a311a8f1fbd2892016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dinitrobenzene 40V, Positive-QTOFsplash10-03xu-1900000000-8fe9c8f85ceb745b09622016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dinitrobenzene 10V, Negative-QTOFsplash10-014i-0900000000-b1ee7d966d12380fc8d42016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dinitrobenzene 20V, Negative-QTOFsplash10-014i-0900000000-66896cdfc20c56dcfd5d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dinitrobenzene 40V, Negative-QTOFsplash10-014i-1900000000-648609457021263ea5ad2016-08-03Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
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 IDDB02680
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID7172
KEGG Compound IDNot Available
BioCyc ID13-DINITROBENZENE
BiGG IDNot Available
Wikipedia Link1,3-Dinitrobenzene
METLIN IDNot Available
PubChem Compound7452
PDB IDNot Available
ChEBI ID51397
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 ]