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


Ligand Structure Quality Assessment 


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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2A,
B [auth C],
C [auth E]
96Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00987
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 
D [auth A],
E [auth C],
F [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
0R3 Binding MOAD:  4ERF Kd: 0.4 (nM) from 1 assay(s)
BindingDB:  4ERF Kd: 0.4 (nM) from 1 assay(s)
IC50: min: 1, max: 10 (nM) from 4 assay(s)
PDBBind:  4ERF Kd: 0.4 (nM) from 1 assay(s)
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



Ligand Structure Quality Assessment 



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