co-crystal structure of MDM2 (17-111) in complex with compound 25

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.214 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

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Discovery of AMG 232, a Potent, Selective, and Orally Bioavailable MDM2-p53 Inhibitor in Clinical Development.

Sun, D.Li, Z.Rew, Y.Gribble, M.Bartberger, M.D.Beck, H.P.Canon, J.Chen, A.Chen, X.Chow, D.Deignan, J.Duquette, J.Eksterowicz, J.Fisher, B.Fox, B.M.Fu, J.Gonzalez, A.Z.Gonzalez-Lopez De Turiso, F.Houze, J.B.Huang, X.Jiang, M.Jin, L.Kayser, F.Liu, J.J.Lo, M.C.Long, A.M.Lucas, B.McGee, L.R.McIntosh, J.Mihalic, J.Oliner, J.D.Osgood, T.Peterson, M.L.Roveto, P.Saiki, A.Y.Shaffer, P.Toteva, M.Wang, Y.Wang, Y.C.Wortman, S.Yakowec, P.Yan, X.Ye, Q.Yu, D.Yu, M.Zhao, X.Zhou, J.Zhu, J.Olson, S.H.Medina, J.C.

(2014) J Med Chem 57: 1454-1472

  • DOI: https://doi.org/10.1021/jm401753e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We recently reported the discovery of AM-8553 (1), a potent and selective piperidinone inhibitor of the MDM2-p53 interaction. Continued research investigation of the N-alkyl substituent of this series, focused in particular on a previously underutilized interaction in a shallow cleft on the MDM2 surface, led to the discovery of a one-carbon tethered sulfone which gave rise to substantial improvements in biochemical and cellular potency. Further investigation produced AMG 232 (2), which is currently being evaluated in human clinical trials for the treatment of cancer. Compound 2 is an extremely potent MDM2 inhibitor (SPR KD = 0.045 nM, SJSA-1 EdU IC50 = 9.1 nM), with remarkable pharmacokinetic properties and in vivo antitumor activity in the SJSA-1 osteosarcoma xenograft model (ED50 = 9.1 mg/kg).

  • 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 Mdm2A,
B [auth C],
C [auth E]
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
PHAROS:  Q00987
GTEx:  ENSG00000135679 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00987
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2SW

Download Ideal Coordinates CCD File 
D [auth A],
E [auth C],
F [auth E]
[(3R,5R,6S)-1-[(2S)-1-(tert-butylsulfonyl)butan-2-yl]-5-(3-chlorophenyl)-6-(4-chlorophenyl)-3-methyl-2-oxopiperidin-3-yl]acetic acid
C28 H35 Cl2 N O5 S
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
2SW BindingDB:  4OAS Kd: 0.04 (nM) from 1 assay(s)
IC50: min: 0.1, max: 18 (nM) from 3 assay(s)
Binding MOAD:  4OAS Kd: 0.05 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.214 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.554α = 90
b = 99.035β = 90
c = 107.076γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2014-02-19 
  • Deposition Author(s): Huang, X.

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations