4HG7

Crystal Structure of an MDM2/Nutlin-3a complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

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This is version 1.1 of the entry. See complete history. 


Literature

The structure of an MDM2-Nutlin-3a complex solved by the use of a validated MDM2 surface-entropy reduction mutant.

Anil, B., Riedinger, C., Endicott, J.A., Noble, M.E.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1358-1366

  • DOI: 10.1107/S0907444913004459
  • Primary Citation of Related Structures:  
    4HFZ, 4HG7

  • PubMed Abstract: 

    • The p53-binding site of MDM2 holds great promise as a target for therapeutic intervention in MDM2-amplified p53 wild-type forms of cancer. Despite the extensive validation of this strategy, there are relatively few crystallographically determined co- ...

    The p53-binding site of MDM2 holds great promise as a target for therapeutic intervention in MDM2-amplified p53 wild-type forms of cancer. Despite the extensive validation of this strategy, there are relatively few crystallographically determined co-complex structures for small-molecular inhibitors of the MDM2-p53 interaction available in the PDB. Here, a surface-entropy reduction mutant of the N-terminal domain of MDM2 that has been designed to enhance crystallogenesis is presented. This mutant has been validated by comparative ligand-binding studies using differential scanning fluorimetry and fluorescence polarization anisotropy and by cocrystallization with a peptide derived from p53. Using this mutant, the cocrystal structure of MDM2 with the benchmark inhibitor Nutlin-3a has been determined, revealing subtle differences from the previously described co-complex of MDM2 with Nutlin-2.

    Organizational Affiliation: 

    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2A97Homo sapiensMutation(s): 2 
Gene Names: MDM2
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q00987 (Homo sapiens)
Explore Q00987 
Go to UniProtKB:  Q00987
NIH Common Fund Data Resources
PHAROS  Q00987
GTEx  ENSG00000135679
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NUT
Query on NUT
Download Ideal Coordinates CCD File 
A
4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one
C30 H30 Cl2 N4 O4
BDUHCSBCVGXTJM-WUFINQPMSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NUTKi:  6.400000095367432   nM  BindingDB
NUTKd:  700   nM  BindingDB
NUTKi:  36   nM  BindingDB
NUTKd:  35   nM  BindingDB
NUTIC50:  18   nM  BindingDB
NUTKi:  30   nM  BindingDB
NUTIC50:  90   nM  Binding MOAD
NUTKi:  11   nM  BindingDB
NUTKi:  20   nM  BindingDB
NUTIC50:  10   nM  BindingDB
NUTIC50:  180   nM  BindingDB
NUTIC50:  100   nM  BindingDB
NUTIC50:  105   nM  BindingDB
NUTKi:  140   nM  BindingDB
NUTIC50:  70   nM  BindingDB
NUTKi:  110   nM  BindingDB
NUTIC50:  88   nM  BindingDB
NUTIC50:  89   nM  BindingDB
NUTIC50:  90   nM  BindingDB
NUTKi:  121   nM  BindingDB
NUTIC50:  13600   nM  BindingDB
NUTIC50:  61   nM  BindingDB
NUTIC50 :  90   nM  PDBBind
NUTKi:  90   nM  BindingDB
NUTIC50:  600   nM  BindingDB
NUTIC50:  610   nM  BindingDB
NUTKi:  59   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.45α = 90
b = 71.45β = 90
c = 104.204γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-08-21
    Changes: Database references