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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 11.80 kDa 
• Atom Count: 913 
• Modelled Residue Count: 94 
• Deposited Residue Count: 94 
• Unique protein chains: 1

4MDN

Structure of a novel submicromolar MDM2 inhibitor

• PDB DOI: 10.2210/pdb4MDN/pdb

• Classification: LIGASE/LIGASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-08-23 Released: 2013-11-13 
• Deposition Author(s): Bista, M., Popowicz, G., Holak, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.203 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

Literature

Transient Protein States in Designing Inhibitors of the MDM2-p53 Interaction.

Bista, M., Wolf, S., Khoury, K., Kowalska, K., Huang, Y., Wrona, E., Arciniega, M., Popowicz, G.M., Holak, T.A., Domling, A.

(2013) Structure 21: 2143-2151

• PubMed: 24207125 
• DOI: 10.1016/j.str.2013.09.006
• Primary Citation of Related Structures:  
  4MDN, 4MDQ


• PubMed Abstract: 
  

Reactivation of p53 by release of the functional protein from its inhibition by MDM2 provides an efficient, nongenotoxic approach to a wide variety of cancers. We present the cocrystal structures of two complexes of MDM2 with inhibitors based on 6-chloroindole scaffolds. Both molecules bound to a distinct conformational state of MDM2 with nM-μM affinities. In contrast to other structurally characterized antagonists, which mimic three amino acids of p53 (Phe19, Trp23, and Leu26), the compounds induced an additional hydrophobic pocket on the MDM2 surface and unveiled a four-point binding mode. The enlarged interaction interface of the inhibitors resulted in extension of small molecules binding toward the "lid" segment of MDM2 (residues 19-23)--a nascent element that interferes with p53 binding. As supported by protein engineering and molecular dynamics studies, employing these unstable elements of MDM2 provides an efficient and yet unexplored alternative in development of MDM2-p53 association inhibitors.

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Organizational Affiliation: 

Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A	94	Homo sapiens	Mutation(s): 0  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
Y30	B [auth A]	3-{(1S)-2-(tert-butylamino)-1-[{4-[(4-chlorobenzyl)oxy]benzyl}(formyl)amino]-2-oxoethyl}-6-chloro-1H-indole-2-carboxylic acid C30 H29 Cl2 N3 O5 PESUUIPTWNTJKA-MHZLTWQESA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
Y30	Binding MOAD:  4MDN	Ki: 600 (nM) from 1 assay(s)
	PDBBind:  4MDN	Ki: 600 (nM) from 1 assay(s)
	BindingDB:  4MDN	Ki: 600 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.203 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.341	α = 90
b = 64.341	β = 90
c = 81.685	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-23 
• Released Date: 2013-11-13 
Deposition Author(s): Bista, M., Popowicz, G., Holak, T.A.

Revision History  

• Version 1.0: 2013-11-13
  Type: Initial release
  
• Version 1.1: 2013-12-04
  Changes: Database references
• Version 1.2: 2013-12-25
  Changes: Database references