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Showing metabocard for 3,5-Dinitrocatechol (HMDB0246069)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:06:29 UTC
Update Date2021-09-26 22:54:55 UTC
HMDB IDHMDB0246069
Secondary Accession NumbersNone
Metabolite Identification
Common Name3,5-Dinitrocatechol
Description3,5-Dinitrocatechol belongs to the class of organic compounds known as dinitrophenols. These are organic aromatic compounds containing a benzene that carries a single phenol group and exactly two nitro groups. Based on a literature review very few articles have been published on 3,5-Dinitrocatechol. This compound has been identified in human blood as reported by (PMID: 31557052 ). 3,5-dinitrocatechol is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 3,5-Dinitrocatechol 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 HMDB0246069 (3,5-Dinitrocatechol)

  Mrv0541 02231215582D          

 14 14  0  0  0  0            999 V2000
    2.1434    1.2375    0.0000 O   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
    0.0000    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
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    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
  3  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
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
  4 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
M  CHG  4   9   1  10  -1  12   1  13  -1
M  END
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3D MOL for HMDB0246069 (3,5-Dinitrocatechol)

HMDB0246069
     RDKit          3D
3,5-Dinitrocatechol
 18 18  0  0  0  0  0  0  0  0999 V2000
    3.6223   -0.6101   -0.0577 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8646    0.3659    0.0833 N   0  0  0  0  0  4  0  0  0  0  0  0
    3.4425    1.5940    0.2736 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.4480    0.2458    0.0541 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6633    1.3662    0.2181 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6964    1.3167    0.2004 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4933    2.4555    0.3670 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3567    0.1072    0.0121 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7232    0.0891   -0.0018 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6053   -1.0303   -0.1542 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2176   -2.2954   -0.3531 N   0  0  0  0  0  4  0  0  0  0  0  0
   -2.2951   -2.6296    0.1442 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5744   -3.2320   -1.1454 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.7980   -0.9403   -0.1303 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1143    2.3577    0.3720 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0031    3.3287    0.5039 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3648   -0.6405   -0.1223 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3769   -1.8484   -0.2638 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  1  0
  6  8  2  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 10 14  2  0
 14  4  1  0
  5 15  1  0
  7 16  1  0
  9 17  1  0
 14 18  1  0
M  CHG  4   2   1   3  -1  11   1  13  -1
M  END
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3D SDF for HMDB0246069 (3,5-Dinitrocatechol)

  Mrv0541 02231215582D          

 14 14  0  0  0  0            999 V2000
    2.1434    1.2375    0.0000 O   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
    0.0000    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
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    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
  3  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
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
  4 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
M  CHG  4   9   1  10  -1  12   1  13  -1
M  END
> <DATABASE_ID>
HMDB0246069

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=CC(=CC(=C1O)[N+]([O-])=O)[N+]([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H4N2O6/c9-5-2-3(7(11)12)1-4(6(5)10)8(13)14/h1-2,9-10H

> <INCHI_KEY>
VDCDWNDTNSWDFJ-UHFFFAOYSA-N

> <FORMULA>
C6H4N2O6

> <MOLECULAR_WEIGHT>
200.1058

> <EXACT_MASS>
200.00693587

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
15.389681486859555

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,5-dinitrobenzene-1,2-diol

> <ALOGPS_LOGP>
1.71

> <JCHEM_LOGP>
1.2460835513333333

> <ALOGPS_LOGS>
-2.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.979424082631887

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.384927669374355

> <JCHEM_PKA_STRONGEST_BASIC>
-6.472067423103327

> <JCHEM_POLAR_SURFACE_AREA>
132.1

> <JCHEM_REFRACTIVITY>
44.6692

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.05e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,5-dinitrocatechol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0246069 (3,5-Dinitrocatechol)

HMDB0246069
     RDKit          3D
3,5-Dinitrocatechol
 18 18  0  0  0  0  0  0  0  0999 V2000
    3.6223   -0.6101   -0.0577 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8646    0.3659    0.0833 N   0  0  0  0  0  4  0  0  0  0  0  0
    3.4425    1.5940    0.2736 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.4480    0.2458    0.0541 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6633    1.3662    0.2181 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6964    1.3167    0.2004 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4933    2.4555    0.3670 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3567    0.1072    0.0121 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7232    0.0891   -0.0018 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6053   -1.0303   -0.1542 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2176   -2.2954   -0.3531 N   0  0  0  0  0  4  0  0  0  0  0  0
   -2.2951   -2.6296    0.1442 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5744   -3.2320   -1.1454 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.7980   -0.9403   -0.1303 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1143    2.3577    0.3720 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0031    3.3287    0.5039 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3648   -0.6405   -0.1223 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3769   -1.8484   -0.2638 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  1  0
  6  8  2  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 10 14  2  0
 14  4  1  0
  5 15  1  0
  7 16  1  0
  9 17  1  0
 14 18  1  0
M  CHG  4   2   1   3  -1  11   1  13  -1
M  END
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PDB for HMDB0246069 (3,5-Dinitrocatechol)

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       4.001   2.310   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0      -1.334   2.310   0.000  0.00  0.00           N+1
HETATM   10  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O-1
HETATM   11  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0       1.334  -2.310   0.000  0.00  0.00           N+1
HETATM   13  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O-1
HETATM   14  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   12                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    9                                                  
CONECT    7    6    2    8                                                  
CONECT    8    7                                                            
CONECT    9    6   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    4   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END
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3D PDB for HMDB0246069 (3,5-Dinitrocatechol)

COMPND    HMDB0246069
HETATM    1  O1  UNL     1       3.622  -0.610  -0.058  1.00  0.00           O  
HETATM    2  N1  UNL     1       2.865   0.366   0.083  1.00  0.00           N1+
HETATM    3  O2  UNL     1       3.443   1.594   0.274  1.00  0.00           O1-
HETATM    4  C1  UNL     1       1.448   0.246   0.054  1.00  0.00           C  
HETATM    5  C2  UNL     1       0.663   1.366   0.218  1.00  0.00           C  
HETATM    6  C3  UNL     1      -0.696   1.317   0.200  1.00  0.00           C  
HETATM    7  O3  UNL     1      -1.493   2.455   0.367  1.00  0.00           O  
HETATM    8  C4  UNL     1      -1.357   0.107   0.012  1.00  0.00           C  
HETATM    9  O4  UNL     1      -2.723   0.089  -0.002  1.00  0.00           O  
HETATM   10  C5  UNL     1      -0.605  -1.030  -0.154  1.00  0.00           C  
HETATM   11  N2  UNL     1      -1.218  -2.295  -0.353  1.00  0.00           N1+
HETATM   12  O5  UNL     1      -2.295  -2.630   0.144  1.00  0.00           O  
HETATM   13  O6  UNL     1      -0.574  -3.232  -1.145  1.00  0.00           O1-
HETATM   14  C6  UNL     1       0.798  -0.940  -0.130  1.00  0.00           C  
HETATM   15  H1  UNL     1       1.114   2.358   0.372  1.00  0.00           H  
HETATM   16  H2  UNL     1      -1.003   3.329   0.504  1.00  0.00           H  
HETATM   17  H3  UNL     1      -3.365  -0.641  -0.122  1.00  0.00           H  
HETATM   18  H4  UNL     1       1.377  -1.848  -0.264  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    4    5    5   14
CONECT    5    6   15
CONECT    6    7    8    8
CONECT    7   16
CONECT    8    9   10
CONECT    9   17
CONECT   10   11   14   14
CONECT   11   12   12   13
CONECT   14   18
END
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SMILES for HMDB0246069 (3,5-Dinitrocatechol)

OC1=CC(=CC(=C1O)[N+]([O-])=O)[N+]([O-])=O
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INCHI for HMDB0246069 (3,5-Dinitrocatechol)

InChI=1S/C6H4N2O6/c9-5-2-3(7(11)12)1-4(6(5)10)8(13)14/h1-2,9-10H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
35-DinitrocatecholHMDB
3,5-DinitropyrocatecholHMDB
Chemical FormulaC6H4N2O6
Average Molecular Weight200.1058
Monoisotopic Molecular Weight200.00693587
IUPAC Name3,5-dinitrobenzene-1,2-diol
Traditional Name3,5-dinitrocatechol
CAS Registry NumberNot Available
SMILES
OC1=CC(=CC(=C1O)[N+]([O-])=O)[N+]([O-])=O
InChI Identifier
InChI=1S/C6H4N2O6/c9-5-2-3(7(11)12)1-4(6(5)10)8(13)14/h1-2,9-10H
InChI KeyVDCDWNDTNSWDFJ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dinitrophenols. These are organic aromatic compounds containing a benzene that carries a single phenol group and exactly two nitro groups.
KingdomOrganic compounds
Super ClassBenzenoids
ClassPhenols
Sub ClassNitrophenols
Direct ParentDinitrophenols
Alternative Parents
Substituents
  • Dinitrophenol
  • Nitrobenzene
  • Nitroaromatic compound
  • Catechol
  • 1-hydroxy-4-unsubstituted benzenoid
  • 1-hydroxy-2-unsubstituted benzenoid
  • Monocyclic benzene moiety
  • C-nitro compound
  • Organic nitro compound
  • Organic oxoazanium
  • Allyl-type 1,3-dipolar organic compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic 1,3-dipolar compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External DescriptorsNot Available
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
Predicted Chromatographic Properties
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 IDDB02105
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID3094995
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound3870203
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 ]