1TTV

NMR Structure of a Complex Between MDM2 and a Small Molecule Inhibitor


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 42 
  • Conformers Submitted: 18 
  • Selection Criteria: structures with acceptable covalent geometry,structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

NMR structure of a complex between MDM2 and a small molecule inhibitor.

Fry, D.C.Emerson, S.D.Palme, S.Vu, B.T.Liu, C.M.Podlaski, F.

(2004) J.Biomol.Nmr 30: 163-173

  • DOI: 10.1023/B:JNMR.0000048856.84603.9b

  • PubMed Abstract: 
  • MDM2 is a regulator of cell growth processes that acts by binding to the tumor suppressor protein p53 and ultimately restraining its activity. While inactivation of p53 by mutation is commonly observed in human cancers, a substantial percentage of tu ...

    MDM2 is a regulator of cell growth processes that acts by binding to the tumor suppressor protein p53 and ultimately restraining its activity. While inactivation of p53 by mutation is commonly observed in human cancers, a substantial percentage of tumors express wild type p53. In many of these cases, MDM2 is overexpressed, and it is believed that suppression of MDM2 activity could yield therapeutic benefits. Therefore, we have been focusing on the p53-MDM2 interaction as the basis of a drug discovery program and have been able to develop a series of small molecule inhibitors. We herein report a high resolution NMR structure of a complex between the p53-binding domain of MDM2 and one of these inhibitors. The form of MDM2 utilized was an engineered hybrid between the human and Xenopus sequences, which provided a favorable combination of relevancy and stability. The inhibitor is found to bind in the same site as does a highly potent peptide fragment of p53. The inhibitor is able to successfully mimic the peptide by duplicating interactions in three subpockets normally made by amino acid sidechains, and by utilizing a scaffold that presents substituents with rigidity and spatial orientation comparable to that provided by the alpha helical backbone of the peptide. The structure also suggests opportunities for modifying the inhibitor to increase its potency.


    Organizational Affiliation

    Roche Research Center, Hoffmann-La Roche, Inc. 340 Kingsland Street, Nutley, NJ 07110, USA. david.fry@roche.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-protein ligase E3 Mdm2
A
107Xenopus laevisMutation(s): 3 
Gene Names: mdm2
EC: 2.3.2.27
Find proteins for P56273 (Xenopus laevis)
Go to UniProtKB:  P56273
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMY
Query on IMY

Download SDF File 
Download CCD File 
A
1-{[4,5-BIS(4-CHLOROPHENYL)-2-(2-ISOPROPOXY-4-METHOXYPHENYL)-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]CARBONYL}PIPERAZINE
CIS-[4,5-BIS-(4-CHLOROPHENYL)-2-(2-ISOPROPOXY-4-METHOXYPHENYL)-4,5-DIHYD ROIMIDAZOL-1-YL]-PIPERAZIN-1-YL-METHANONE
C30 H32 Cl2 N4 O3
ZXIPEZDMQNYFOO-WUFINQPMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IMYIC50: 160 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 42 
  • Conformers Submitted: 18 
  • Selection Criteria: structures with acceptable covalent geometry,structures with the least restraint violations 
  • Olderado: 1TTV Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance