4QOC | pdb_00004qoc

crystal structure of compound 16 bound to MDM2(17-111), {(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(1S)-1-CYCLOPROPYL-2-(PYRROLIDIN-1-YLSULFONYL)ETHYL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.253 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.247 (DCC) 

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Ligand Structure Quality Assessment 


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Literature

Optimization beyond AMG 232: discovery and SAR of sulfonamides on a piperidinone scaffold as potent inhibitors of the MDM2-p53 protein-protein interaction.

Wang, Y., Zhu, J., Liu, J.J., Chen, X., Mihalic, J., Deignan, J., Yu, M., Sun, D., Kayser, F., McGee, L.R., Lo, M.C., Chen, A., Zhou, J., Ye, Q., Huang, X., Long, A.M., Yakowec, P., Oliner, J.D., Olson, S.H., Medina, J.C.

(2014) Bioorg Med Chem Lett 24: 3782-3785

  • DOI: https://doi.org/10.1016/j.bmcl.2014.06.073
  • Primary Citation Related Structures: 
    4QOC

  • PubMed Abstract: 

    We recently reported on the discovery of AMG 232, a potent and selective piperidinone inhibitor of the MDM2-p53 interaction. AMG 232 is being evaluated in human clinical trials for cancer. Continued exploration of the N-alkyl substituent of this series, in an effort to optimize interactions with the MDM2 glycine-58 shelf region, led to the discovery of sulfonamides such as compounds 31 and 38 that have similar potency, hepatocyte stability and rat pharmacokinetic properties to AMG 232.

    • Organizational Affiliation: 
    • Department of Therapeutic Discovery, Amgen Inc., 1120 Veterans Boulevard, South San Francisco, CA 94080, USA.

Macromolecule Content 

  • Total Structure Weight: 70.5 kDa 
  • Atom Count: 5,403 
  • Modeled Residue Count: 561 
  • Deposited Residue Count: 576 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm296Homo 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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.253 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.247 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.576α = 90
b = 98.925β = 90
c = 103.921γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2015-05-06 
    • Deposition Author(s): Huang, X.

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations