4QO4 | pdb_00004qo4

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

• PDB DOI: https://doi.org/10.2210/pdb4QO4/pdb

• Classification: Ligase/Ligase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-06-19 Released: 2014-07-16 
• Deposition Author(s): Huang, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.302 (Depositor), 0.313 (DCC) 
• R-Value Work: 
  0.264 (Depositor), 0.263 (DCC) 

Literature

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

• PubMed: 25147610 
• DOI: https://doi.org/10.1021/ml500142b
• Primary Citation Related Structures: 
  4QO4


• 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.

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Organizational Affiliation: 
• Departments of Therapeutic Discovery and Pharmacokinetics and Drug Metabolism, Amgen Inc. , 1120 Veterans Boulevard, South San Francisco, California 94080, United States.
Departments of Therapeutic Discovery and Oncology Research, Amgen Inc. , One Amgen Center Drive, Thousand Oaks, California 91320, United States.
Department of Therapeutic Discovery, Amgen Inc. , 360 Binney Street, Cambridge, Massachusetts 02142, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 11.71 kDa 
• Atom Count: 845 
• Modeled Residue Count: 89 
• Deposited Residue Count: 96 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A	96	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
35S	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 QHQNRLZCHQCYRC-IEPITWRRSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.302 (Depositor), 0.313 (DCC) 
• R-Value Work:  0.264 (Depositor), 0.263 (DCC) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.727	α = 90
b = 56.727	β = 90
c = 102.382	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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