3VBG

Structure of hDM2 with Dimer Inducing Indolyl Hydantoin RO-2443


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 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


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

  • DOI: https://doi.org/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.


  • Organizational Affiliation

    Roche Research Center, Hoffmann-La Roche Inc., Nutley, NJ 07110, USA. bradford.graves@roche.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2
A, B, C, D
85Homo sapiensMutation(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
GTEx:  ENSG00000135679 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00987
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
03M BindingDB:  3VBG IC50: 33 (nM) from 1 assay(s)
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 = 64.392α = 90
b = 64.392β = 90
c = 167.587γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description