4OQ3 | pdb_00004oq3

Tetra-substituted imidazoles as a new class of inhibitors of the p53-MDM2 interaction

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.224 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

Literature

Tetra-substituted imidazoles as a new class of inhibitors of the p53-MDM2 interaction.

Vaupel, A., Bold, G., De Pover, A., Stachyra-Valat, T., Hergovich-Lisztwan, J., Kallen, J., Masuya, K., Furet, P.

(2014) Bioorg Med Chem Lett 24: 2110-2114

  • DOI: https://doi.org/10.1016/j.bmcl.2014.03.039
  • Primary Citation Related Structures: 
    4OQ3

  • PubMed Abstract: 

    Capitalizing on crystal structure information obtained from a previous effort in the search for non peptide inhibitors of the p53-MDM2 interaction, we have discovered another new class of compounds able to disrupt this protein-protein interaction, an important target in oncology drug research. The new inhibitors, based on a tetra-substituted imidazole scaffold, have been optimized to low nanomolar potency in a biochemical assay following a structure-guided approach. An appropriate strategy has allowed us to translate the high biochemical potency in significant anti-proliferative activity on a p53-dependent MDM2 amplified cell line.

    • Organizational Affiliation: 
    • Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland. Electronic address: andrea.vaupel@novartis.com.

Macromolecule Content 

  • Total Structure Weight: 46.44 kDa 
  • Atom Count: 3,343 
  • Modeled Residue Count: 367 
  • Deposited Residue Count: 384 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2
A, B, C, D
96Homo sapiensMutation(s): 1 
Gene Names: MDM2
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens)
Explore Q00987 
Go to UniProtKB:  Q00987
PHAROS:  Q00987
GTEx:  ENSG00000135679 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00987
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.224 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.814α = 90
b = 165.528β = 95.06
c = 34.236γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2014-04-23 
    • Deposition Author(s): Kallen, J.

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-23
    Type: Initial release
  • Version 1.1: 2014-05-21
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description