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Showing NP-Card for 5-[(6-bromo-1h-indol-3-yl)methylidene]imidazole-2,4-diol (NP0321020)

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Record Information
Version2.0
Created at2022-09-11 23:00:11 UTC
Updated at2022-09-11 23:00:11 UTC
NP-MRD IDNP0321020
Secondary Accession NumbersNone
Natural Product Identification
Common Name5-[(6-bromo-1h-indol-3-yl)methylidene]imidazole-2,4-diol
Description4-[(6-Bromo-1H-indol-3-yl)methylidene]-4H-imidazole-2,5-diol belongs to the class of organic compounds known as hydantoins. These are heterocyclic compounds containing an imidazolidine substituted by ketone group at positions 2 and 4. 5-[(6-bromo-1h-indol-3-yl)methylidene]imidazole-2,4-diol is found in Hymeniacidon perlevis. 4-[(6-Bromo-1H-indol-3-yl)methylidene]-4H-imidazole-2,5-diol is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0321020 (5-[(6-bromo-1h-indol-3-yl)methylidene]imidazole-2,4-diol)


  Mrv1533004171520132D          

 18 20  0  0  0  0            999 V2000
    4.0668    2.3479    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -0.1006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2587   -0.8543    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0792   -0.7681    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6313   -1.3812    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2508    0.0389    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5363    0.4514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4500    1.2719    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   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
  7  6  1  4  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
  8 13  1  0  0  0  0
 13 14  2  0  0  0  0
  6 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
  5 17  1  0  0  0  0
 17 18  2  0  0  0  0
  2 18  1  0  0  0  0
M  END
Download

3D MOL for NP0321020 (5-[(6-bromo-1h-indol-3-yl)methylidene]imidazole-2,4-diol)

     RDKit          3D

 26 28  0  0  0  0  0  0  0  0999 V2000
    4.9612    1.4983    0.3343 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1050    0.5647    0.4132 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4338   -0.7016    0.9678 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2366   -1.4568    0.8795 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1187   -2.6463    1.2716 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1713   -0.6423    0.2655 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9274   -1.0223    0.0345 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0943   -0.1918   -0.5663 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0340    0.6404   -1.6587 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2596    1.1995   -1.8598 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1273    0.7694   -0.9425 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4707    1.0429   -0.7228 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0760    0.4142    0.3418 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9339    0.7389    0.7157 Br  0  0  0  0  0  0  0  0  0  0  0  0
   -3.3994   -0.4567    1.1731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0659   -0.7112    0.9333 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4256   -0.0948   -0.1304 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7530    0.6214   -0.0148 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3244   -1.0617    1.3660 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6401   -2.0295    0.3095 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8514    0.8223   -2.2648 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5099    1.8693   -2.6143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0469    1.7115   -1.3388 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8687   -0.9565    2.0181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4846   -1.3834    1.5512 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2736    1.4621   -0.4621 H   0  0  0  0  0  0  0  0  0  0  0  0
 14 13  1  0
 13 15  2  0
 15 16  1  0
 16 17  2  0
 17 11  1  0
 11 10  1  0
 10  9  1  0
  9  8  2  0
  8  7  1  0
  7  6  2  0
  6 18  1  0
 18  2  1  0
  2  1  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
 11 12  2  0
 12 13  1  0
  8 17  1  0
  4  6  1  0
 15 24  1  0
 16 25  1  0
 10 22  1  0
  9 21  1  0
  7 20  1  0
 18 26  1  0
  3 19  1  0
 12 23  1  0
M  END
Download

3D SDF for NP0321020 (5-[(6-bromo-1h-indol-3-yl)methylidene]imidazole-2,4-diol)


  Mrv1533004171520132D          

 18 20  0  0  0  0            999 V2000
    4.0668    2.3479    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -0.1006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2587   -0.8543    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0792   -0.7681    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6313   -1.3812    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2508    0.0389    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5363    0.4514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4500    1.2719    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   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
  7  6  1  4  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
  8 13  1  0  0  0  0
 13 14  2  0  0  0  0
  6 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
  5 17  1  0  0  0  0
 17 18  2  0  0  0  0
  2 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0321020

> <DATABASE_NAME>
NP-MRD

> <SMILES>
BrC1=CC=C2C(NC=C2C=C2NC(=O)NC2=O)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C12H8BrN3O2/c13-7-1-2-8-6(5-14-9(8)4-7)3-10-11(17)16-12(18)15-10/h1-5,14H,(H2,15,16,17,18)

> <INCHI_KEY>
LUYXYXVNRFZRHK-UHFFFAOYSA-N

> <FORMULA>
C12H8BrN3O2

> <MOLECULAR_WEIGHT>
306.119

> <EXACT_MASS>
304.97999

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
26.55975061164682

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-[(6-bromo-1H-indol-3-yl)methylidene]imidazolidine-2,4-dione

> <ALOGPS_LOGP>
2.11

> <JCHEM_LOGP>
1.5450173753333334

> <ALOGPS_LOGS>
-3.81

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.223999304334402

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.393539486433313

> <JCHEM_PKA_STRONGEST_BASIC>
-5.8056559966408035

> <JCHEM_POLAR_SURFACE_AREA>
73.99000000000001

> <JCHEM_REFRACTIVITY>
70.4368

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.78e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-[(6-bromo-1H-indol-3-yl)methylidene]imidazolidine-2,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0321020 (5-[(6-bromo-1h-indol-3-yl)methylidene]imidazole-2,4-diol)

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PDB for NP0321020 (5-[(6-bromo-1h-indol-3-yl)methylidene]imidazole-2,4-diol)
HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1 Br   UNK     0       7.591   4.383   0.000  0.00  0.00          Br+0
HETATM    2  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.143  -0.188   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -0.483  -1.595   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      -2.015  -1.434   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -3.045  -2.578   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0      -2.335   0.073   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      -1.001   0.843   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -0.840   2.374   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   18                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   17                                                  
CONECT    6    5    7   15                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12    8   14                                                  
CONECT   14   13                                                            
CONECT   15    6   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16    5   18                                                  
CONECT   18   17    2                                                       
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

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3D PDB for NP0321020 (5-[(6-bromo-1h-indol-3-yl)methylidene]imidazole-2,4-diol)
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SMILES for NP0321020 (5-[(6-bromo-1h-indol-3-yl)methylidene]imidazole-2,4-diol)
BrC1=CC=C2C(NC=C2C=C2NC(=O)NC2=O)=C1
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INCHI for NP0321020 (5-[(6-bromo-1h-indol-3-yl)methylidene]imidazole-2,4-diol)
InChI=1S/C12H8BrN3O2/c13-7-1-2-8-6(5-14-9(8)4-7)3-10-11(17)16-12(18)15-10/h1-5,14H,(H2,15,16,17,18)
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SynonymsNot Available
Chemical FormulaC12H8BrN3O2
Average Mass306.1190 Da
Monoisotopic Mass304.97999 Da
IUPAC Name5-[(6-bromo-1H-indol-3-yl)methylidene]imidazolidine-2,4-dione
Traditional Name5-[(6-bromo-1H-indol-3-yl)methylidene]imidazolidine-2,4-dione
CAS Registry NumberNot Available
SMILES
BrC1=CC=C2C(NC=C2C=C2NC(=O)NC2=O)=C1
InChI Identifier
InChI=1S/C12H8BrN3O2/c13-7-1-2-8-6(5-14-9(8)4-7)3-10-11(17)16-12(18)15-10/h1-5,14H,(H2,15,16,17,18)
InChI KeyLUYXYXVNRFZRHK-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Hymeniacidon perlevisLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hydantoins. These are heterocyclic compounds containing an imidazolidine  substituted by ketone group at positions 2 and 4.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassAzolidines  
Sub ClassImidazolidines  
Direct ParentHydantoins  
Alternative Parents
Substituents
  • Hydantoin
    • 

  • Alpha-amino acid or derivatives
    • 

  • Indole
    • 

  • Indole or derivatives
    • 

  • 5-monosubstituted hydantoin
    • 

  • N-acyl urea
    • 

  • Ureide
    • 

  • Aryl bromide
    • 

  • Aryl halide
    • 

  • Substituted pyrrole
    • 

  • Benzenoid
    • 

  • Pyrrole
    • 

  • Heteroaromatic compound
    • 

  • Dicarboximide
    • 

  • Urea
    • 

  • Carbonic acid derivative
    • 

  • Azacycle
    • 

  • Carboxylic acid derivative
    • 

  • Organic nitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Organohalogen compound
    • 

  • Organobromide
    • 

  • Carbonyl group
    • 

  • Organonitrogen compound
    • 

  • Organooxygen compound
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
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
logP2.11ALOGPS
logP1.55ChemAxon
logS-3.8ALOGPS
pKa (Strongest Acidic)7.39ChemAxon
pKa (Strongest Basic)-5.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area73.99 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity70.44 m³·mol⁻¹ChemAxon
Polarizability26.56 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound74051198  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]