Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.85 kDa 
• Atom Count: 2941 
• Modelled Residue Count: 338 
• Deposited Residue Count: 340 
• Unique protein chains: 1

3VBG

Structure of hDM2 with Dimer Inducing Indolyl Hydantoin RO-2443

• PDB DOI: 10.2210/pdb3VBG/pdb

• Classification: Ligase/ligase activator
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2012-01-02 Released: 2012-06-27 
• Deposition Author(s): Lukacs, C.M., Janson, C.A., Graves, B.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.220 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Activation of the p53 pathway by small-molecule-induced MDM2 and MDMX dimerization.

Graves, B., Thompson, T., Xia, M., Janson, C., Lukacs, C., Deo, D., Di Lello, P., Fry, D., Garvie, C., Huang, K.S., Gao, L., Tovar, C., Lovey, A., Wanner, J., Vassilev, L.T.

(2012) Proc Natl Acad Sci U S A 109: 11788-11793

• PubMed: 22745160 
• DOI: 10.1073/pnas.1203789109
• Primary Citation of Related Structures:  
  3U15, 3VBG


• PubMed Abstract: 
  

Activation of p53 tumor suppressor by antagonizing its negative regulator murine double minute (MDM)2 has been considered an attractive strategy for cancer therapy and several classes of p53-MDM2 binding inhibitors have been developed. However, these compounds do not inhibit the p53-MDMX interaction, and their effectiveness can be compromised in tumors overexpressing MDMX. Here, we identify small molecules that potently block p53 binding with both MDM2 and MDMX by inhibitor-driven homo- and/or heterodimerization of MDM2 and MDMX proteins. Structural studies revealed that the inhibitors bind into and occlude the p53 pockets of MDM2 and MDMX by inducing the formation of dimeric protein complexes kept together by a dimeric small-molecule core. This mode of action effectively stabilized p53 and activated p53 signaling in cancer cells, leading to cell cycle arrest and apoptosis. Dual MDM2/MDMX antagonists restored p53 apoptotic activity in the presence of high levels of MDMX and may offer a more effective therapeutic modality for MDMX-overexpressing cancers.

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Organizational Affiliation: 

Roche Research Center, Hoffmann-La Roche Inc., Nutley, NJ 07110, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A, B, C, D	85	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
03M	E [auth A], F [auth B], G [auth C], H [auth D]	(5Z)-5-[(6-chloro-7-methyl-1H-indol-3-yl)methylidene]-3-(3,4-difluorobenzyl)imidazolidine-2,4-dione C20 H14 Cl F2 N3 O2 OEXMEVPQEPHTAQ-IDUWFGFVSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
03M	PDBBind:  3VBG	IC50: 33 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.220 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.392	α = 90
b = 64.392	β = 90
c = 167.587	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-02 
• Released Date: 2012-06-27 
Deposition Author(s): Lukacs, C.M., Janson, C.A., Graves, B.J.

Revision History  

• Version 1.0: 2012-06-27
  Type: Initial release
  
• Version 1.1: 2012-07-25
  Changes: Database references
• Version 1.2: 2012-08-01
  Changes: Database references
• Version 1.3: 2019-07-17
  Changes: Data collection, Refinement description