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Showing NP-Card for Debromo-Z-axinohydantoin (NP0076409)

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Record Information
Version2.0
Created at2022-04-28 21:33:24 UTC
Updated at2022-04-28 21:33:24 UTC
NP-MRD IDNP0076409
Secondary Accession NumbersNone
Natural Product Identification
Common NameDebromo-Z-axinohydantoin
DescriptionSpongiacidin C 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. Debromo-Z-axinohydantoin is found in Stylissa massa and Stylotella aurantium. Debromo-Z-axinohydantoin was first documented in 2013 (PMID: 23684893). Based on a literature review very few articles have been published on spongiacidin C.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0076409 (Debromo-Z-axinohydantoin)


  Mrv1652304282223332D          

 18 20  0  0  0  0            999 V2000
    4.1569    1.7738    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5149    1.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1569    0.2872    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3526    0.1036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1690   -0.7007    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7076    0.6180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7076    1.4430    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3526    1.9574    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1690    2.7617    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4104    3.0859    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4844    3.9076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8631    4.4504    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2887    4.0912    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7118    3.3830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5335    3.3090    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9230    1.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4380    1.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9230    0.3631    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  1  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
  9 14  1  0  0  0  0
 14 15  2  0  0  0  0
  7 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
  6 18  1  0  0  0  0
M  END
Download

3D MOL for NP0076409 (Debromo-Z-axinohydantoin)

     RDKit          3D

 28 30  0  0  0  0  0  0  0  0999 V2000
    4.4020    1.5062   -0.8464 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5320    0.7019   -0.4188 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7785   -0.5971    0.0729 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5285   -1.1496    0.4466 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4223   -2.2994    0.9216 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4746   -0.1524    0.1749 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1772   -0.3524    0.3257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2422   -1.6966    0.7880 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6895   -2.0121    0.6189 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3185   -1.6567   -0.6082 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5885   -0.3248   -1.0789 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4508   -0.0985   -1.9261 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8721    0.8553   -0.5961 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2517    2.1407   -0.6280 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3076    2.9007   -0.0230 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2524    2.0935    0.4327 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6298    0.8443    0.0615 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1189    0.9957   -0.3665 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7246   -1.0703    0.1481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0209   -1.7591    1.8685 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3040   -2.4828    0.1873 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2280   -1.5944    1.5178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7912   -3.1141    0.7320 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6556   -2.3887   -1.2939 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1520    2.4283   -1.0712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3758    3.9663    0.0824 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6183    2.4204    0.9789 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7456    1.8957   -0.7282 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  6 18  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 13 17  2  0
 17 16  1  0
 16 15  2  0
 15 14  1  0
 18  2  1  0
 17  7  1  0
 14 13  1  0
  3 19  1  0
 18 28  1  0
  8 20  1  0
  8 21  1  0
  9 22  1  0
  9 23  1  0
 10 24  1  0
 16 27  1  0
 15 26  1  0
 14 25  1  0
M  END
Download

3D SDF for NP0076409 (Debromo-Z-axinohydantoin)


  Mrv1652304282223332D          

 18 20  0  0  0  0            999 V2000
    4.1569    1.7738    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5149    1.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1569    0.2872    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3526    0.1036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1690   -0.7007    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7076    0.6180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7076    1.4430    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3526    1.9574    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1690    2.7617    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4104    3.0859    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4844    3.9076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8631    4.4504    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2887    4.0912    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7118    3.3830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5335    3.3090    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9230    1.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4380    1.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9230    0.3631    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  1  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
  9 14  1  0  0  0  0
 14 15  2  0  0  0  0
  7 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
  6 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0076409

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O=C1NC(=O)\C(N1)=C1/CCNC(=O)C2=C1C=CN2

> <INCHI_IDENTIFIER>
InChI=1S/C11H10N4O3/c16-9-7-5(1-3-12-7)6(2-4-13-9)8-10(17)15-11(18)14-8/h1,3,12H,2,4H2,(H,13,16)(H2,14,15,17,18)/b8-6-

> <INCHI_KEY>
MOYLWFAZPQYOGQ-VURMDHGXSA-N

> <FORMULA>
C11H10N4O3

> <MOLECULAR_WEIGHT>
246.226

> <EXACT_MASS>
246.075290198

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
23.1168408193154

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-[(4Z)-8-oxo-1H,4H,5H,6H,7H,8H-pyrrolo[2,3-c]azepin-4-ylidene]imidazolidine-2,4-dione

> <ALOGPS_LOGP>
0.03

> <JCHEM_LOGP>
-1.4224339246666668

> <ALOGPS_LOGS>
-2.69

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.167268329623813

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.233305498968371

> <JCHEM_PKA_STRONGEST_BASIC>
-1.2134745037195644

> <JCHEM_POLAR_SURFACE_AREA>
103.09

> <JCHEM_REFRACTIVITY>
62.8893

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.05e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-[(4Z)-8-oxo-1H,5H,6H,7H-pyrrolo[2,3-c]azepin-4-ylidene]imidazolidine-2,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0076409 (Debromo-Z-axinohydantoin)

Download
PDB for NP0076409 (Debromo-Z-axinohydantoin)
HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       7.760   3.311   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.428   1.924   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       7.760   0.536   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       6.258   0.193   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.916  -1.308   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       5.054   1.154   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.054   2.694   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.258   3.654   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.916   5.155   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       4.499   5.760   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       4.637   7.294   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       3.478   8.307   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0       6.139   7.637   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       6.929   6.315   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       8.463   6.177   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       3.590   3.169   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.684   1.924   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0       3.590   0.678   0.000  0.00  0.00           N+0
CONECT    1    2    8                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   18                                                  
CONECT    7    6    8   16                                                  
CONECT    8    7    1    9                                                  
CONECT    9    8   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13    9   15                                                  
CONECT   15   14                                                            
CONECT   16    7   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17    6                                                       
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

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3D PDB for NP0076409 (Debromo-Z-axinohydantoin)
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SMILES for NP0076409 (Debromo-Z-axinohydantoin)
O=C1NC(=O)\C(N1)=C1/CCNC(=O)C2=C1C=CN2
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INCHI for NP0076409 (Debromo-Z-axinohydantoin)
InChI=1S/C11H10N4O3/c16-9-7-5(1-3-12-7)6(2-4-13-9)8-10(17)15-11(18)14-8/h1,3,12H,2,4H2,(H,13,16)(H2,14,15,17,18)/b8-6-
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View in JSmol
SynonymsNot Available
Chemical FormulaC11H10N4O3
Average Mass246.2260 Da
Monoisotopic Mass246.07529 Da
IUPAC Name5-[(4Z)-8-oxo-1H,4H,5H,6H,7H,8H-pyrrolo[2,3-c]azepin-4-ylidene]imidazolidine-2,4-dione
Traditional Name5-[(4Z)-8-oxo-1H,5H,6H,7H-pyrrolo[2,3-c]azepin-4-ylidene]imidazolidine-2,4-dione
CAS Registry NumberNot Available
SMILES
O=C1NC(=O)\C(N1)=C1/CCNC(=O)C2=C1C=CN2
InChI Identifier
InChI=1S/C11H10N4O3/c16-9-7-5(1-3-12-7)6(2-4-13-9)8-10(17)15-11(18)14-8/h1,3,12H,2,4H2,(H,13,16)(H2,14,15,17,18)/b8-6-
InChI KeyMOYLWFAZPQYOGQ-VURMDHGXSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Stylissa massaLOTUS Database
Stylotella aurantiumPlant
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
    • 

  • Pyrroloazepine
    • 

  • 2-heteroaryl carboxamide
    • 

  • 5-monosubstituted hydantoin
    • 

  • Azepine
    • 

  • N-acyl urea
    • 

  • Ureide
    • 

  • Dicarboximide
    • 

  • Pyrrole
    • 

  • Heteroaromatic compound
    • 

  • Secondary carboxylic acid amide
    • 

  • Carbonic acid derivative
    • 

  • Lactam
    • 

  • Carboxamide group
    • 

  • Urea
    • 

  • Carboxylic acid derivative
    • 

  • Azacycle
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Organic nitrogen compound
    • 

  • Carbonyl group
    • 

  • Organic oxygen 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
logP0.03ALOGPS
logP-1.4ChemAxon
logS-2.7ALOGPS
pKa (Strongest Acidic)7.23ChemAxon
pKa (Strongest Basic)-1.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area103.09 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity62.89 m³·mol⁻¹ChemAxon
Polarizability23.12 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00038953  
Chemspider ID8809507  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10634145  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Yamaguchi M, Miyazaki M, Kodrasov MP, Rotinsulu H, Losung F, Mangindaan RE, de Voogd NJ, Yokosawa H, Nicholson B, Tsukamoto S: Spongiacidin C, a pyrrole alkaloid from the marine sponge Stylissa massa, functions as a USP7 inhibitor. Bioorg Med Chem Lett. 2013 Jul 1;23(13):3884-6. doi: 10.1016/j.bmcl.2013.04.066.  Epub 2013 May 3. [PubMed:23684893  ]