co-crystal structure of MDM2 (17-111) with compound 16, {(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(1S)-1-(6-CYCLOPROPYLPYRIDIN-2-YL)PROPYL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.264 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Discovery of Potent and Simplified Piperidinone-Based Inhibitors of the MDM2-p53 Interaction.

Yu, M.Wang, Y.Zhu, J.Bartberger, M.D.Canon, J.Chen, A.Chow, D.Eksterowicz, J.Fox, B.Fu, J.Gribble, M.Huang, X.Li, Z.Liu, J.J.Lo, M.C.McMinn, D.Oliner, J.D.Osgood, T.Rew, Y.Saiki, A.Y.Shaffer, P.Yan, X.Ye, Q.Yu, D.Zhao, X.Zhou, J.Olson, S.H.Medina, J.C.Sun, D.

(2014) ACS Med Chem Lett 5: 894-899

  • DOI: https://doi.org/10.1021/ml500142b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Continued optimization of the N-substituent in the piperidinone series provided potent piperidinone-pyridine inhibitors 6, 7, 14, and 15 with improved pharmacokinetic properties in rats. Reducing structure complexity of the N-alkyl substituent led to the discovery of 23, a potent and simplified inhibitor of MDM2. Compound 23 exhibits excellent pharmacokinetic properties and substantial in vivo antitumor activity in the SJSA-1 osteosarcoma xenograft mouse model.

  • Organizational Affiliation

    Departments of Therapeutic Discovery 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 Mdm296Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 35S

Download Ideal Coordinates CCD File 
B [auth A]{(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(1S)-1-(6-cyclopropylpyridin-2-yl)propyl]-3-methyl-2-oxopiperidin-3-yl}acetic acid
C31 H32 Cl2 N2 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.264 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.727α = 90
b = 56.727β = 90
c = 102.382γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2014-07-16 
  • Deposition Author(s): Huang, X.

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-09-10
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations