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Showing metabocard for 1-Nitro-5,6-dihydroxy-dihydronaphthalene (HMDB0060328)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-05-17 00:54:01 UTC
Update Date2022-03-07 03:17:43 UTC
HMDB IDHMDB0060328
Secondary Accession Numbers
  • HMDB60328
Metabolite Identification
Common Name1-Nitro-5,6-dihydroxy-dihydronaphthalene
Description1-Nitro-5,6-dihydroxy-dihydronaphthalene, also known as 1,2-dihydro-5-nitro-1,2-naphthalenediol, belongs to the class of organic compounds known as nitronaphthalenes. These are polycyclic aromatic compounds containing a naphthalene moiety substituted by one or more nitro groups. 1-Nitro-5,6-dihydroxy-dihydronaphthalene is an extremely weak basic (essentially neutral) compound (based on its pKa). 1-Nitro-5,6-dihydroxy-dihydronaphthalene exists in all living organisms, ranging from bacteria to humans. These are polycyclic aromatic compounds containing a naphthalene moiety substituted by one or more nitro groups.
Structure
Data?1563866045
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0060328 (1-Nitro-5,6-dihydroxy-dihydronaphthalene)

  Mrv0541 05161317542D          

 15 16  0  0  0  0            999 V2000
   -0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    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
    2.1434    1.2375    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 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
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  5  4  2  0  0  0  0
  6  4  1  0  0  0  0
  7  2  1  0  0  0  0
  7  6  2  0  0  0  0
  8  3  2  0  0  0  0
  8  6  1  0  0  0  0
  9  5  1  0  0  0  0
 10  7  1  0  0  0  0
 10  9  1  0  0  0  0
 11  8  1  0  0  0  0
 12  9  1  0  0  0  0
 13 10  1  0  0  0  0
 14 11  2  0  0  0  0
 15 11  2  0  0  0  0
M  END
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3D MOL for HMDB0060328 (1-Nitro-5,6-dihydroxy-dihydronaphthalene)

HMDB0060328
     RDKit          3D
1-Nitro-5,6-dihydroxy-dihydronaphthalene
 24 25  0  0  0  0  0  0  0  0999 V2000
    3.9463   -0.7828    1.4979 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9342   -1.0515    0.7908 N   0  0  0  0  0  4  0  0  0  0  0  0
    2.7679   -2.3544    0.4656 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.0380   -0.0495    0.3755 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5245    1.2515    0.1564 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6827    2.2544   -0.2460 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3500    2.0192   -0.4463 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1465    0.7102   -0.2266 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6951   -0.3046    0.1810 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1052   -1.6107    0.4483 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1951   -1.8348    0.3107 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1588   -0.8078   -0.1147 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9435   -1.2773   -1.2011 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5737    0.4868   -0.4772 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3016    1.5367    0.1442 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5610    1.4050    0.3200 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0547    3.2786   -0.4198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3390    2.7858   -0.7636 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7371   -2.4249    0.7854 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6227   -2.8306    0.5157 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8746   -0.6442    0.7555 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3612   -2.1449   -0.9049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7576    0.6976   -1.5842 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1221    1.6922   -0.3626 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  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
  9  4  1  0
 14  8  1  0
  5 16  1  0
  6 17  1  0
  7 18  1  0
 10 19  1  0
 11 20  1  0
 12 21  1  0
 13 22  1  0
 14 23  1  0
 15 24  1  0
M  CHG  2   2   1   3  -1
M  END
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3D SDF for HMDB0060328 (1-Nitro-5,6-dihydroxy-dihydronaphthalene)

  Mrv0541 05161317542D          

 15 16  0  0  0  0            999 V2000
   -0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    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
    2.1434    1.2375    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 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
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  5  4  2  0  0  0  0
  6  4  1  0  0  0  0
  7  2  1  0  0  0  0
  7  6  2  0  0  0  0
  8  3  2  0  0  0  0
  8  6  1  0  0  0  0
  9  5  1  0  0  0  0
 10  7  1  0  0  0  0
 10  9  1  0  0  0  0
 11  8  1  0  0  0  0
 12  9  1  0  0  0  0
 13 10  1  0  0  0  0
 14 11  2  0  0  0  0
 15 11  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060328

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1C=CC2=C(C=CC=C2N(=O)=O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C10H9NO4/c12-9-5-4-6-7(10(9)13)2-1-3-8(6)11(14)15/h1-5,9-10,12-13H

> <INCHI_KEY>
VNMNNCGXMBPWIX-UHFFFAOYSA-N

> <FORMULA>
C10H9NO4

> <MOLECULAR_WEIGHT>
207.1828

> <EXACT_MASS>
207.053157781

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
19.136368668674397

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-nitro-1,2-dihydronaphthalene-1,2-diol

> <ALOGPS_LOGP>
0.76

> <JCHEM_LOGP>
0.9364553406666669

> <ALOGPS_LOGS>
-1.69

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.635595839789609

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.028130916972515

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3837855279770563

> <JCHEM_POLAR_SURFACE_AREA>
86.28

> <JCHEM_REFRACTIVITY>
54.7045

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.25e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-nitro-1,2-dihydronaphthalene-1,2-diol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0060328 (1-Nitro-5,6-dihydroxy-dihydronaphthalene)

HMDB0060328
     RDKit          3D
1-Nitro-5,6-dihydroxy-dihydronaphthalene
 24 25  0  0  0  0  0  0  0  0999 V2000
    3.9463   -0.7828    1.4979 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9342   -1.0515    0.7908 N   0  0  0  0  0  4  0  0  0  0  0  0
    2.7679   -2.3544    0.4656 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.0380   -0.0495    0.3755 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5245    1.2515    0.1564 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6827    2.2544   -0.2460 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3500    2.0192   -0.4463 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1465    0.7102   -0.2266 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6951   -0.3046    0.1810 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1052   -1.6107    0.4483 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1951   -1.8348    0.3107 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1588   -0.8078   -0.1147 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9435   -1.2773   -1.2011 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5737    0.4868   -0.4772 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3016    1.5367    0.1442 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5610    1.4050    0.3200 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0547    3.2786   -0.4198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3390    2.7858   -0.7636 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7371   -2.4249    0.7854 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6227   -2.8306    0.5157 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8746   -0.6442    0.7555 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3612   -2.1449   -0.9049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7576    0.6976   -1.5842 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1221    1.6922   -0.3626 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  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
  9  4  1  0
 14  8  1  0
  5 16  1  0
  6 17  1  0
  7 18  1  0
 10 19  1  0
 11 20  1  0
 12 21  1  0
 13 22  1  0
 14 23  1  0
 15 24  1  0
M  CHG  2   2   1   3  -1
M  END
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PDB for HMDB0060328 (1-Nitro-5,6-dihydroxy-dihydronaphthalene)

HEADER    PROTEIN                                 16-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-MAY-13         0                                  
HETATM    1  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001   2.310   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       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0       5.335   4.620   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       2.667   6.160   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    7                                                       
CONECT    3    1    8                                                       
CONECT    4    5    6                                                       
CONECT    5    4    9                                                       
CONECT    6    4    7    8                                                  
CONECT    7    2    6   10                                                  
CONECT    8    3    6   11                                                  
CONECT    9    5   10   12                                                  
CONECT   10    7    9   13                                                  
CONECT   11    8   14   15                                                  
CONECT   12    9                                                            
CONECT   13   10                                                            
CONECT   14   11                                                            
CONECT   15   11                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END
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3D PDB for HMDB0060328 (1-Nitro-5,6-dihydroxy-dihydronaphthalene)

COMPND    HMDB0060328
HETATM    1  O1  UNL     1       3.946  -0.783   1.498  1.00  0.00           O  
HETATM    2  N1  UNL     1       2.934  -1.052   0.791  1.00  0.00           N1+
HETATM    3  O2  UNL     1       2.768  -2.354   0.466  1.00  0.00           O1-
HETATM    4  C1  UNL     1       2.038  -0.049   0.375  1.00  0.00           C  
HETATM    5  C2  UNL     1       2.524   1.252   0.156  1.00  0.00           C  
HETATM    6  C3  UNL     1       1.683   2.254  -0.246  1.00  0.00           C  
HETATM    7  C4  UNL     1       0.350   2.019  -0.446  1.00  0.00           C  
HETATM    8  C5  UNL     1      -0.147   0.710  -0.227  1.00  0.00           C  
HETATM    9  C6  UNL     1       0.695  -0.305   0.181  1.00  0.00           C  
HETATM   10  C7  UNL     1       0.105  -1.611   0.448  1.00  0.00           C  
HETATM   11  C8  UNL     1      -1.195  -1.835   0.311  1.00  0.00           C  
HETATM   12  C9  UNL     1      -2.159  -0.808  -0.115  1.00  0.00           C  
HETATM   13  O3  UNL     1      -2.943  -1.277  -1.201  1.00  0.00           O  
HETATM   14  C10 UNL     1      -1.574   0.487  -0.477  1.00  0.00           C  
HETATM   15  O4  UNL     1      -2.302   1.537   0.144  1.00  0.00           O  
HETATM   16  H1  UNL     1       3.561   1.405   0.320  1.00  0.00           H  
HETATM   17  H2  UNL     1       2.055   3.279  -0.420  1.00  0.00           H  
HETATM   18  H3  UNL     1      -0.339   2.786  -0.764  1.00  0.00           H  
HETATM   19  H4  UNL     1       0.737  -2.425   0.785  1.00  0.00           H  
HETATM   20  H5  UNL     1      -1.623  -2.831   0.516  1.00  0.00           H  
HETATM   21  H6  UNL     1      -2.875  -0.644   0.755  1.00  0.00           H  
HETATM   22  H7  UNL     1      -3.361  -2.145  -0.905  1.00  0.00           H  
HETATM   23  H8  UNL     1      -1.758   0.698  -1.584  1.00  0.00           H  
HETATM   24  H9  UNL     1      -3.122   1.692  -0.363  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    4    5    5    9
CONECT    5    6   16
CONECT    6    7    7   17
CONECT    7    8   18
CONECT    8    9    9   14
CONECT    9   10
CONECT   10   11   11   19
CONECT   11   12   20
CONECT   12   13   14   21
CONECT   13   22
CONECT   14   15   23
CONECT   15   24
END
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SMILES for HMDB0060328 (1-Nitro-5,6-dihydroxy-dihydronaphthalene)

OC1C=CC2=C(C=CC=C2N(=O)=O)C1O
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INCHI for HMDB0060328 (1-Nitro-5,6-dihydroxy-dihydronaphthalene)

InChI=1S/C10H9NO4/c12-9-5-4-6-7(10(9)13)2-1-3-8(6)11(14)15/h1-5,9-10,12-13H
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1,2-Dihydro-5-nitro-1,2-naphthalenediolKegg
Chemical FormulaC10H9NO4
Average Molecular Weight207.1828
Monoisotopic Molecular Weight207.053157781
IUPAC Name5-nitro-1,2-dihydronaphthalene-1,2-diol
Traditional Name5-nitro-1,2-dihydronaphthalene-1,2-diol
CAS Registry NumberNot Available
SMILES
OC1C=CC2=C(C=CC=C2N(=O)=O)C1O
InChI Identifier
InChI=1S/C10H9NO4/c12-9-5-4-6-7(10(9)13)2-1-3-8(6)11(14)15/h1-5,9-10,12-13H
InChI KeyVNMNNCGXMBPWIX-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as nitronaphthalenes. These are polycyclic aromatic compounds containing a naphthalene moiety substituted by one or more nitro groups.
KingdomOrganic compounds
Super ClassBenzenoids
ClassNaphthalenes
Sub ClassNitronaphthalenes
Direct ParentNitronaphthalenes
Alternative Parents
Substituents
  • 1-nitronaphthalene
  • Nitroaromatic compound
  • 1,2-diol
  • C-nitro compound
  • Secondary alcohol
  • Organic nitro compound
  • Organic oxoazanium
  • Allyl-type 1,3-dipolar organic compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic 1,3-dipolar compound
  • Organic zwitterion
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Organopnictogen compound
  • Alcohol
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Aromatic homopolycyclic compound
Molecular FrameworkAromatic homopolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
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 LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
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 IDNot Available
KEGG Compound IDC14801
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound11954052
PDB IDNot Available
ChEBI ID34099
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. Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]

Enzymes

Enzyme Details
1. Epoxide hydrolase 1
General function:
Involved in catalytic activity
Specific function:
Biotransformation enzyme that catalyzes the hydrolysis of arene and aliphatic epoxides to less reactive and more water soluble dihydrodiols by the trans addition of water.
Gene Name:
EPHX1
Uniprot ID:
P07099
Molecular weight:
52948.48
Reactions
1-Nitronaphthalene-5,6-oxide + Water → 1-Nitro-5,6-dihydroxy-dihydronaphthalenedetails