4ERF | pdb_00004erf

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 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.246 (DCC) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/jm300354j
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 34.9 kDa 
  • Atom Count: 2,465 
  • Modeled Residue Count: 278 
  • Deposited Residue Count: 288 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence 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
GTEx:  ENSG00000135679 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00987
Sequence Annotations
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
0R3 BindingDB:  4ERF Kd: 0.4 (nM) from 1 assay(s)
IC50: min: 1, max: 10 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.250 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.246 (DCC) 
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

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • 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
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations