Co-crystal structure of MDM2 with Inhibitor Compound 4

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.288 
  • R-Value Observed: 0.290 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Selective and Potent Morpholinone Inhibitors of the MDM2-p53 Protein-Protein Interaction.

Gonzalez, A.Z.Eksterowicz, J.Bartberger, M.D.Beck, H.P.Canon, J.Chen, A.Chow, D.Duquette, J.Fox, B.M.Fu, J.Huang, X.Houze, J.B.Jin, L.Li, Y.Li, Z.Ling, Y.Lo, M.C.Long, A.M.McGee, L.R.McIntosh, J.McMinn, D.L.Oliner, J.D.Osgood, T.Rew, Y.Saiki, A.Y.Shaffer, P.Wortman, S.Yakowec, P.Yan, X.Ye, Q.Yu, D.Zhao, X.Zhou, J.Olson, S.H.Medina, J.C.Sun, D.

(2014) J Med Chem 57: 2472-2488

  • DOI: https://doi.org/10.1021/jm401767k
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We previously reported the discovery of AMG 232, a highly potent and selective piperidinone inhibitor of the MDM2-p53 interaction. Our continued search for potent and diverse analogues led to the discovery of novel morpholinone MDM2 inhibitors. This change to a morpholinone core has a significant impact on both potency and metabolic stability compared to the piperidinone series. Within this morpholinone series, AM-8735 emerged as an inhibitor with remarkable biochemical potency (HTRF IC50 = 0.4 nM) and cellular potency (SJSA-1 EdU IC50 = 25 nM), as well as pharmacokinetic properties. Compound 4 also shows excellent antitumor activity in the SJSA-1 osteosarcoma xenograft model with an ED50 of 41 mg/kg. Lead optimization toward the discovery of this inhibitor as well as key differences between the morpholinone and the piperidinone series will be described herein.

  • Organizational Affiliation

    Departments of †Therapeutic Discovery, ‡Pharmaceutics, and §Pharmacokinetics and Drug Metabolism, Amgen Inc. , 1120 Veterans Boulevard, South San Francisco, California 94080, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2
A, B, C
96Homo sapiensMutation(s): 0 
Gene Names: MDM2
EC: 6.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens)
Explore Q00987 
Go to UniProtKB:  Q00987
GTEx:  ENSG00000135679 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00987
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2TW

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]
[(2R,5R,6R)-4-[(1S)-2-(tert-butylsulfonyl)-1-cyclopropylethyl]-6-(3-chlorophenyl)-5-(4-chlorophenyl)-3-oxomorpholin-2-yl]acetic acid
C27 H31 Cl2 N O6 S
Binding Affinity Annotations 
IDSourceBinding Affinity
2TW BindingDB:  4OBA IC50: min: 0.4, max: 160 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.288 
  • R-Value Observed: 0.290 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.729α = 90
b = 98.674β = 90
c = 106.687γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-04-09
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description