4ERF

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 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:  
    4ERE, 4ERF

  • 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 N-alkyl substituent ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2 A, C, E96Homo sapiensMutation(s): 0 
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0R3
Query on 0R3
Download Ideal Coordinates 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 :  0.4000000059604645   nM  PDBBind
0R3IC50:  10   nM  BindingDB
0R3Kd:  0.4000000059604645   nM  Binding MOAD
0R3IC50:  1   nM  BindingDB
0R3Kd:  0.4000000059604645   nM  BindingDB
0R3IC50:  4.099999904632568   nM  BindingDB
0R3IC50:  1.100000023841858   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.230 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.77α = 90
b = 97.89β = 90
c = 105.59γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report


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  (Full details and data files)

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