Structure of human MDMX protein in complex with a small molecule inhibitor

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

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This is version 1.4 of the entry. See complete history


Structures of low molecular weight inhibitors bound to MDMX and MDM2 reveal new approaches for p53-MDMX/MDM2 antagonist drug discovery

Popowicz, G.M.Czarna, A.Wolf, S.Wang, K.Wang, W.Domling, A.Holak, T.A.

(2010) Cell Cycle 9: 1104-1111

  • DOI: https://doi.org/10.4161/cc.9.6.10956
  • Primary Citation of Related Structures:  
    3LBJ, 3LBK, 3LBL

  • PubMed Abstract: 

    Intensive anticancer drug discovery efforts have been made to develop small molecule inhibitors of the p53-MDM2 and p53-MDMX interactions. We present here the structures of the most potent inhibitors bound to MDM2 and MDMX that are based on the new imidazo-indole scaffold. In addition, the structure of the recently reported spiro-oxindole inhibitor bound to MDM2 is described. The structures indicate how the substituents of a small molecule that bind to the three subpockets of the MDM2/X-p53 interaction should be optimized for effective binding to MDM2 and/or MDMX. While the spiro-oxindole inhibitor triggers significant ligand-induced changes in MDM2, the imidazo-indoles share similar binding modes for MDMX and MDM2, but cause only minimal induced-fit changes in the structures of both proteins. Our study includes the first structure of the complex between MDMX and a small molecule and should aid in developing efficient scaffolds for binding to MDMX and/or MDM2.

  • Organizational Affiliation

    Max-Planck-Institute of Biochemistry, Martinsried, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein Mdm4A [auth E]90Homo sapiensMutation(s): 0 
Gene Names: MDM4MDMX
UniProt & NIH Common Fund Data Resources
Find proteins for O15151 (Homo sapiens)
Explore O15151 
Go to UniProtKB:  O15151
PHAROS:  O15151
GTEx:  ENSG00000198625 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15151
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on WW8

Download Ideal Coordinates CCD File 
B [auth E],
C [auth E]
C35 H38 Cl2 N6 O
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
WW8 PDBBind:  3LBJ Ki: 1.10e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.97α = 90
b = 80.97β = 90
c = 80.97γ = 90
Software Package:
Software NamePurpose
MAR345data collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2018-10-17
    Changes: Data collection, Database references
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description