4ERF

crystal structure of MDM2 (17-111) in complex with compound 29 (AM-8553)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


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

Literature

Structure-based design of novel inhibitors of the MDM2-p53 interaction.

Rew, Y., Sun, D., Gonzalez-Lopez De Turiso, F., Bartberger, M.D., Beck, H.P., Canon, J., Chen, A., Chow, D., Deignan, J., Fox, B.M., Gustin, D., Huang, X., Jiang, M., Jiao, X., Jin, L., Kayser, F., Kopecky, D.J., Li, Y., Lo, M.C., Long, A.M., Michelsen, K., Oliner, J.D., Osgood, T., Ragains, M., Saiki, A.Y., Schneider, S., Toteva, M., Yakowec, P., Yan, X., Ye, Q., Yu, D., Zhao, X., Zhou, J., Medina, J.C., Olson, S.H.

(2012) J.Med.Chem. 55: 4936-4954

  • DOI: 10.1021/jm300354j
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Structure-based rational design led to the discovery of novel inhibitors of the MDM2-p53 protein-protein interaction. The affinity of these compounds for MDM2 was improved through conformational control of both the piperidinone ring and the appended ...

    Structure-based rational design led to the discovery of novel inhibitors of the MDM2-p53 protein-protein interaction. The affinity of these compounds for MDM2 was improved through conformational control of both the piperidinone ring and the appended N-alkyl substituent. Optimization afforded 29 (AM-8553), a potent and selective MDM2 inhibitor with excellent pharmacokinetic properties and in vivo efficacy.

    Organizational Affiliation: 

    Department of Therapeutic Discovery, Amgen Inc., 1120 Veterans Boulevard, South San Francisco, California 94080, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase Mdm2
A, C, E
96Homo sapiensMutation(s): 0 
Gene Names: MDM2
EC: 2.3.2.27
Find proteins for Q00987 (Homo sapiens)
Go to Gene View: MDM2
Go to UniProtKB:  Q00987
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0R3
Query on 0R3
Download SDF File 
Download CCD File 
A, C, E
{(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S,3S)-2-hydroxypentan-3-yl]-3-methyl-2-oxopiperidin-3-yl}acetic acid
C25 H29 Cl2 N O4
YUALYRLIFVPOHL-VPLUBSIMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0R3Kd: 0.4 nM (100) BINDINGDB
0R3IC50: 1.1 - 4.1 nM (100) BINDINGDB
0R3IC50: 1.1 nM BINDINGMOAD
0R3Kd: 0.4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.230 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 56.770α = 90.00
b = 97.890β = 90.00
c = 105.590γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data collection
AMoREphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2012-04-20 
  • Released Date: 2012-05-23 
  • Deposition Author(s): Huang, X.

Revision History 

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references