Showing metabocard for Phenylhydantoin (MMDBc0030208)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:58:27 UTC
Update Date2024-04-30 19:44:47 UTC
Metabolite IDMMDBc0030208
Metabolite Identification
Common NamePhenylhydantoin
DescriptionPhenylhydantoin is a cyclic ureide and it is believed that E. coli may use these compounds as nutrient sources. The gene hyuA codes for d-stereospecific phenylhydantoinase (465 amino acids) which is a homotetramer. This enzyme belongs to the cyclic amidohydrolase superfamily. E. coli D-phenylhydantoinase exhibits a distinct activity toward phenylhydantoin with an aromatic side chain at the 5' position but does not readily hydrolyze the simple cyclic ureides. D-phenylhydantoinase shares a significant homology (>45%) with those of allantoinase and dihydropyrimidinase.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f923d82a6a0>

Structure #1
  Mrv0541 02241207342D          

 13 14  0  0  0  0            999 V2000
    0.7145    5.9411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    5.5286    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    5.5286    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.7036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    4.7036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.2911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    3.4661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819    2.9812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    2.1965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470    2.9812    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270    2.1965    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1665    3.2361    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830    1.5291    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  2  0  0  0  0
  4  6  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7 10  1  0  0  0  0
  8 11  2  0  0  0  0
  8 12  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  9 13  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f923d82a6a0>

HMDB0246838
     RDKit          3D
5-Phenylhydantoin
 21 22  0  0  0  0  0  0  0  0999 V2000
    3.2515    2.2474    1.1791 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5029    1.0717    0.9567 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3830    0.8571    1.5544 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8861   -0.4144    1.1108 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4135   -0.2255    0.4098 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4470   -1.0853    0.7090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6498   -0.9151    0.0642 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7672    0.1075   -0.8520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7385    0.9706   -1.1560 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5313    0.7948   -0.5046 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9041   -0.8951    0.1604 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8413   -2.0887   -0.5180 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8223   -0.0055    0.1003 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0343    3.0070    0.5346 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7934   -1.1577    1.9255 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3064   -1.8842    1.4451 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4957   -1.5868    0.2819 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7296    0.2281   -1.3548 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9180    1.7447   -1.8873 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2881    1.4634   -0.7307 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2902   -2.2340   -1.3514 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
  4 11  1  0
 11 12  1  0
 11 13  2  0
 13  2  1  0
 10  5  1  0
  1 14  1  0
  4 15  1  0
  6 16  1  0
  7 17  1  0
  8 18  1  0
  9 19  1  0
 10 20  1  0
 12 21  1  0
M  END
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3D SDF for #<Metabolite:0x00007f923d82a6a0>

Structure #1
  Mrv0541 02241207342D          

 13 14  0  0  0  0            999 V2000
    0.7145    5.9411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    5.5286    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    5.5286    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.7036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    4.7036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.2911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    3.4661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819    2.9812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    2.1965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470    2.9812    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270    2.1965    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1665    3.2361    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830    1.5291    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  2  0  0  0  0
  4  6  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7 10  1  0  0  0  0
  8 11  2  0  0  0  0
  8 12  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  9 13  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030208

> <DATABASE_NAME>
MIME

> <SMILES>
OC1=NC(C(O)=N1)C1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C9H8N2O2/c12-8-7(10-9(13)11-8)6-4-2-1-3-5-6/h1-5,7H,(H2,10,11,12,13)

> <INCHI_KEY>
NXQJDVBMMRCKQG-UHFFFAOYSA-N

> <FORMULA>
C9H8N2O2

> <MOLECULAR_WEIGHT>
176.172

> <EXACT_MASS>
176.05857751

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
17.169638025568087

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-phenyl-4H-imidazole-2,5-diol

> <ALOGPS_LOGP>
0.62

> <JCHEM_LOGP>
1.739613868666667

> <ALOGPS_LOGS>
-2.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.68280134589416

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.517326783288749

> <JCHEM_PKA_STRONGEST_BASIC>
0.03298492173383327

> <JCHEM_POLAR_SURFACE_AREA>
65.18

> <JCHEM_REFRACTIVITY>
46.4474

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.33e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-phenyl-5H-imidazole-2,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f923d82a6a0>

HMDB0246838
     RDKit          3D
5-Phenylhydantoin
 21 22  0  0  0  0  0  0  0  0999 V2000
    3.2515    2.2474    1.1791 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5029    1.0717    0.9567 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3830    0.8571    1.5544 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8861   -0.4144    1.1108 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4135   -0.2255    0.4098 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4470   -1.0853    0.7090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6498   -0.9151    0.0642 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7672    0.1075   -0.8520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7385    0.9706   -1.1560 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5313    0.7948   -0.5046 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9041   -0.8951    0.1604 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8413   -2.0887   -0.5180 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8223   -0.0055    0.1003 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0343    3.0070    0.5346 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7934   -1.1577    1.9255 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3064   -1.8842    1.4451 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4957   -1.5868    0.2819 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7296    0.2281   -1.3548 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9180    1.7447   -1.8873 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2881    1.4634   -0.7307 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2902   -2.2340   -1.3514 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
  4 11  1  0
 11 12  1  0
 11 13  2  0
 13  2  1  0
 10  5  1  0
  1 14  1  0
  4 15  1  0
  6 16  1  0
  7 17  1  0
  8 18  1  0
  9 19  1  0
 10 20  1  0
 12 21  1  0
M  END
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PDB for #<Metabolite:0x00007f923d82a6a0>

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       1.334  11.090   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667  10.320   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  10.320   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   8.780   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   8.780   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   8.010   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   6.470   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.580   5.565   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.564   4.100   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       0.088   5.565   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       2.104   4.100   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0       4.044   6.041   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -0.342   2.854   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    6                                                       
CONECT    6    4    5    7                                                  
CONECT    7    6    8   10                                                  
CONECT    8    7   11   12                                                  
CONECT    9   10   11   13                                                  
CONECT   10    7    9                                                       
CONECT   11    8    9                                                       
CONECT   12    8                                                            
CONECT   13    9                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   28    0
END
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3D PDB for #<Metabolite:0x00007f923d82a6a0>

COMPND    HMDB0246838
HETATM    1  O1  UNL     1       3.251   2.247   1.179  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.503   1.072   0.957  1.00  0.00           C  
HETATM    3  N1  UNL     1       1.383   0.857   1.554  1.00  0.00           N  
HETATM    4  C2  UNL     1       0.886  -0.414   1.111  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.414  -0.226   0.410  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.447  -1.085   0.709  1.00  0.00           C  
HETATM    7  C5  UNL     1      -2.650  -0.915   0.064  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.767   0.108  -0.852  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.738   0.971  -1.156  1.00  0.00           C  
HETATM   10  C8  UNL     1      -0.531   0.795  -0.505  1.00  0.00           C  
HETATM   11  C9  UNL     1       1.904  -0.895   0.160  1.00  0.00           C  
HETATM   12  O2  UNL     1       1.841  -2.089  -0.518  1.00  0.00           O  
HETATM   13  N2  UNL     1       2.822  -0.006   0.100  1.00  0.00           N  
HETATM   14  H1  UNL     1       3.034   3.007   0.535  1.00  0.00           H  
HETATM   15  H2  UNL     1       0.793  -1.158   1.925  1.00  0.00           H  
HETATM   16  H3  UNL     1      -1.306  -1.884   1.445  1.00  0.00           H  
HETATM   17  H4  UNL     1      -3.496  -1.587   0.282  1.00  0.00           H  
HETATM   18  H5  UNL     1      -3.730   0.228  -1.355  1.00  0.00           H  
HETATM   19  H6  UNL     1      -1.918   1.745  -1.887  1.00  0.00           H  
HETATM   20  H7  UNL     1       0.288   1.463  -0.731  1.00  0.00           H  
HETATM   21  H8  UNL     1       1.290  -2.234  -1.351  1.00  0.00           H  
CONECT    1    2   14
CONECT    2    3    3   13
CONECT    3    4
CONECT    4    5   11   15
CONECT    5    6    6   10
CONECT    6    7   16
CONECT    7    8    8   17
CONECT    8    9   18
CONECT    9   10   10   19
CONECT   10   20
CONECT   11   12   13   13
CONECT   12   21
END
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SMILES for #<Metabolite:0x00007f923d82a6a0>

OC1=NC(C(O)=N1)C1=CC=CC=C1
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INCHI for #<Metabolite:0x00007f923d82a6a0>

InChI=1S/C9H8N2O2/c12-8-7(10-9(13)11-8)6-4-2-1-3-5-6/h1-5,7H,(H2,10,11,12,13)
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Synonyms
ValueSource
5-Phenylhydantoin sodiumHMDB
5-Phenylhydantoin, (+-)-isomerHMDB
5-Phenylhydantoin, (R)-isomerHMDB
5-Phenylhydantoin, (S)-isomerHMDB
5-PhenylhydantoinMeSH
Molecular FormulaC9H8N2O2
Average Mass176.172
Monoisotopic Mass176.05857751
IUPAC Name4-phenyl-4H-imidazole-2,5-diol
Traditional Name5-phenyl-5H-imidazole-2,4-diol
CAS Registry Number89-24-7
SMILES
OC1=NC(C(O)=N1)C1=CC=CC=C1
InChI Identifier
InChI=1S/C9H8N2O2/c12-8-7(10-9(13)11-8)6-4-2-1-3-5-6/h1-5,7H,(H2,10,11,12,13)
InChI KeyNXQJDVBMMRCKQG-UHFFFAOYSA-N