4DIJ

The Central Valine Concept Provides an Entry in a New Class of Non Peptide Inhibitors of the P53-MDM2 Interaction

• PDB DOI: https://doi.org/10.2210/pdb4DIJ/pdb

• Classification: LIGASE/LIGASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-01-31 Released: 2012-05-02 
• Deposition Author(s): Kallen, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.224 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Starting Model: other

Literature

The central valine concept provides an entry in a new class of non peptide inhibitors of the p53-MDM2 interaction.

Furet, P., Chene, P., De Pover, A., Valat, T.S., Lisztwan, J.H., Kallen, J., Masuya, K.

(2012) Bioorg Med Chem Lett 22: 3498-3502

• PubMed: 22507962 
• DOI: https://doi.org/10.1016/j.bmcl.2012.03.083
• Primary Citation of Related Structures:  
  4DIJ


• PubMed Abstract: 
  

  Disrupting the interaction between the p53 tumor suppressor and its regulator MDM2 is a promising therapeutic strategy in anticancer drug research. In our search for non peptide inhibitors of this protein-protein interaction, we have devised a ligand design concept exploiting the central position of Val 93 in the p53 binding pocket of MDM2. The design of molecules based on this concept has allowed us to rapidly identify compounds having a 3-imidazolyl indole core structure as the first representatives of a new class of potent inhibitors of the p53-MDM2 interaction.

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Organizational Affiliation: 

Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.49 kDa 
• Atom Count: 1,813 
• Modelled Residue Count: 186 
• Deposited Residue Count: 192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A, B	96	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BLF	C [auth A], D [auth B]	6-chloro-3-[1-(4-chlorobenzyl)-4-phenyl-1H-imidazol-5-yl]-N-[2-(morpholin-4-yl)ethyl]-1H-indole-2-carboxamide C31 H29 Cl2 N5 O2 IFORBTVIRBZFON-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BLF	PDBBind:  4DIJ	IC50: 30 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.224 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.234	α = 90
b = 38.234	β = 90
c = 175.151	γ = 90

Software Package:

Software Name	Purpose
RemDAq	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-02 
Deposition Author(s): Kallen, J.

Revision History  

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2012-05-23
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description