4ZGK

Structure of Mdm2 with low molecular weight inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.188 

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
  • Primary Citation of Related Structures:  

  • 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

    Faculty of Mathematics and Natural Sciences, Department of Pharmacy, University of Groningen , 9713AV Groningen, The Netherlands.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Gronostajowa 7, 30-387 Krakow, Poland.,Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland.,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: 2.3.2.27
Find proteins for Q00987 (Homo sapiens)
Go to Gene View: MDM2
Go to UniProtKB:  Q00987
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4NX
Query on 4NX

Download SDF File 
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: <1000 - 3100 nM (100) BINDINGDB
4NXKd: 3100 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.610α = 90.00
b = 56.550β = 90.00
c = 97.310γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALAdata scaling
REFMACrefinement
PHASERphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references