Biological Assembly 1  

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

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

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 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 11.76 kDa 
• Atom Count: 932 
• Modelled Residue Count: 91 
• Deposited Residue Count: 97 
• Unique protein chains: 1

4HG7

Crystal Structure of an MDM2/Nutlin-3a complex

• PDB DOI: 10.2210/pdb4HG7/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-10-07 Released: 2013-07-31 
• Deposition Author(s): Noble, M.E.M., Anil, B., Riedinger, C., Endicott, J.A.

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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 

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

• PubMed: 23897459 
• 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-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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A	97	Homo sapiens	Mutation(s): 2  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NUT	B [auth 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
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
NUT	BindingDB:  4HG7	Ki: min: 6.4, max: 140 (nM) from 11 assay(s)
		Kd: min: 35, max: 700 (nM) from 3 assay(s)
		IC50: min: 10, max: 3.00e+4 (nM) from 14 assay(s)
	Binding MOAD:  4HG7	IC50: 90 (nM) from 1 assay(s)
	PDBBind:  4HG7	IC50: 90 (nM) from 1 assay(s)

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 = 71.45	α = 90
b = 71.45	β = 90
c = 104.204	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-07 
• Released Date: 2013-07-31 
Deposition Author(s): Noble, M.E.M., Anil, B., Riedinger, C., Endicott, J.A.

Revision History  

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