4ERE | pdb_00004ere

crystal structure of MDM2 (17-111) in complex with compound 23

• PDB DOI: https://doi.org/10.2210/pdb4ERE/pdb

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


• Deposited: 2012-04-20 Released: 2012-05-23 
• Deposition Author(s): Huang, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.270 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.277 (DCC) 

Literature

Structure-based design of novel inhibitors of the MDM2-p53 interaction.

Rew, Y., Sun, D., Gonzalez-Lopez De Turiso, F., Bartberger, M.D., Beck, H.P., Canon, J., Chen, A., Chow, D., Deignan, J., Fox, B.M., Gustin, D., Huang, X., Jiang, M., Jiao, X., Jin, L., Kayser, F., Kopecky, D.J., Li, Y., Lo, M.C., Long, A.M., Michelsen, K., Oliner, J.D., Osgood, T., Ragains, M., Saiki, A.Y., Schneider, S., Toteva, M., Yakowec, P., Yan, X., Ye, Q., Yu, D., Zhao, X., Zhou, J., Medina, J.C., Olson, S.H.

(2012) J Med Chem 55: 4936-4954

• PubMed: 22524527 
• DOI: https://doi.org/10.1021/jm300354j
• Primary Citation Related Structures: 
  4ERE, 4ERF


• PubMed Abstract: 
  

  Structure-based rational design led to the discovery of novel inhibitors of the MDM2-p53 protein-protein interaction. The affinity of these compounds for MDM2 was improved through conformational control of both the piperidinone ring and the appended N-alkyl substituent. Optimization afforded 29 (AM-8553), a potent and selective MDM2 inhibitor with excellent pharmacokinetic properties and in vivo efficacy.

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Organizational Affiliation: 
• Department of Therapeutic Discovery, Amgen Inc., 1120 Veterans Boulevard, South San Francisco, California 94080, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.45 kDa 
• Atom Count: 1,667 
• Modeled Residue Count: 175 
• Deposited Residue Count: 192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A, B	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0R2	C [auth A], E [auth B]	[(3R,5R,6S)-1-[(2S)-1-tert-butoxy-1-oxobutan-2-yl]-5-(3-chlorophenyl)-6-(4-chlorophenyl)-2-oxopiperidin-3-yl]acetic acid C27 H31 Cl2 N O5 ZEMLYWMOSZRCQL-UWSZBUKDSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
0R2	BindingDB:  4ERE	IC50: min: 4, max: 40 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.270 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.277 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.15	α = 90
b = 60.24	β = 90
c = 68.09	γ = 90

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: 2012-05-23 
Deposition Author(s): Huang, X.

Revision History  

• Version 1.0: 2012-05-23
  Type: Initial release
  
• Version 1.1: 2013-01-02
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations