4ZGK

Structure of Mdm2 with low molecular weight inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A Unique Mdm2-Binding Mode of the 3-Pyrrolin-2-one- and 2-Furanone-Based Antagonists of the p53-Mdm2 Interaction.

Surmiak, E.Twarda-Clapa, A.Zak, K.M.Musielak, B.Tomala, M.D.Kubica, K.Grudnik, P.Madej, M.Jablonski, M.Potempa, J.Kalinowska-Tluscik, J.Domling, A.Dubin, G.Holak, T.A.

(2016) ACS Chem Biol 11: 3310-3318

  • DOI: 10.1021/acschembio.6b00596
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The p53 pathway is inactivated in almost all types of cancer by mutations in the p53 encoding gene or overexpression of the p53 negative regulators, Mdm2 and/or Mdmx. Restoration of the p53 function by inhibition of the p53-Mdm2/Mdmx interaction open ...

    The p53 pathway is inactivated in almost all types of cancer by mutations in the p53 encoding gene or overexpression of the p53 negative regulators, Mdm2 and/or Mdmx. Restoration of the p53 function by inhibition of the p53-Mdm2/Mdmx interaction opens up a prospect for a nongenotoxic anticancer therapy. Here, we present the syntheses, activities, and crystal structures of two novel classes of Mdm2-p53 inhibitors that are based on the 3-pyrrolin-2-one and 2-furanone scaffolds. The structures of the complexes formed by these inhibitors and Mdm2 reveal the dimeric protein molecular organization that has not been observed in the small-molecule/Mdm2 complexes described until now. In particular, the 6-chloroindole group does not occupy the usual Trp-23 pocket of Mdm2 but instead is engaged in dimerization. This entirely unique binding mode of the compounds opens new possibilities for optimization of the Mdm2-p53 interaction inhibitors.


    Organizational Affiliation

    Malopolska Centre of Biotechnology, Jagiellonian University , Gronostajowa 7a, 30-387 Krakow, Poland.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase Mdm2
A, B
98Homo sapiensMutation(s): 0 
Gene Names: MDM2
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q00987 (Homo sapiens)
Go to UniProtKB:  Q00987
NIH Common Fund Data Resources
PHAROS  Q00987
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4NX
Query on 4NX

Download CCD File 
A, B
(5R)-3,5-bis(4-chlorobenzyl)-4-(6-chloro-1H-indol-3-yl)-5-hydroxyfuran-2(5H)-one
C26 H18 Cl3 N O3
MLBSWDQJORDIOB-AREMUKBSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4NXKd:  3100   nM  BindingDB
4NXKd:  3100   nM  Binding MOAD
4NXKd:  1000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.61α = 90
b = 56.55β = 90
c = 97.31γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Foundation for Polish SciencePolandTEAM/2011-8/2
National Centre of SciencePolandUMO-2011/01/D/NZ1/01169

Revision History 

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Database references