Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 11.65 kDa 
• Atom Count: 864 
• Modelled Residue Count: 83 
• Deposited Residue Count: 90 
• Unique protein chains: 1

3LBJ

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

• DOI: 10.2210/pdb3LBJ/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-01-08 Released: 2010-03-16 
• Deposition Author(s): Popowicz, G.M., Czarna, A., Wolf, S., Holak, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.206 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Literature

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

• PubMed: 20237429 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Mdm4	E	90	Homo sapiens	Mutation(s): 0  Gene Names: MDM4, MDMX
Find proteins for O15151 (Homo sapiens) Explore O15151  Go to UniProtKB:  O15151
NIH Common Fund Data Resources
PHAROS:  O15151 GTEx:  ENSG00000198625

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WW8	E	N-[(3S)-1-({6-chloro-3-[1-(4-chlorobenzyl)-4-phenyl-1H-imidazol-5-yl]-1H-indol-2-yl}carbonyl)pyrrolidin-3-yl]-N,N',N'-trimethylpropane-1,3-diamine C35 H38 Cl2 N6 O LWWQYOWAPGRPRH-NDEPHWFRSA-N
SO4	E	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
WW8	Ki :  11000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 80.97	α = 90
b = 80.97	β = 90
c = 80.97	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-01-08 
• Released Date: 2010-03-16 
Deposition Author(s): Popowicz, G.M., Czarna, A., Wolf, S., Holak, T.A.

Revision History  

• 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