4JV7

Co-crystal structure of MDM2 with inhibitor (2S,5R,6S)-2-benzyl-5,6-bis(4-bromophenyl)-4-methylmorpholin-3-one

• PDB DOI:  https://doi.org/10.2210/pdb4JV7/pdb

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


• Deposited: 2013-03-25 Released: 2013-05-01 
• Deposition Author(s): Huang, X., Gonzalez-Lopez de Turiso, F., Sun, D., Yosup, R., Bartberger, M.D., Beck, H.P., Cannon, J., Shaffer, P., Oliner, J.D., Olson, S.H., Medina, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.281 
• R-Value Work: 0.230 

Literature

Rational Design and Binding Mode Duality of MDM2-p53 Inhibitors.

Gonzalez-Lopez de Turiso, F., Sun, D., Rew, Y., Bartberger, M.D., Beck, H.P., Canon, J., Chen, A., Chow, D., Correll, T.L., Huang, X., Julian, L.D., Kayser, F., Lo, M.C., Long, A.M., McMinn, D., Oliner, J.D., Osgood, T., Powers, J.P., Saiki, A.Y., Schneider, S., Shaffer, P., Xiao, S.H., Yakowec, P., Yan, X., Ye, Q., Yu, D., Zhao, X., Zhou, J., Medina, J.C., Olson, S.H.

(2013) J Med Chem 56: 4053-4070

• PubMed: 23597064 
• DOI: https://doi.org/10.1021/jm400293z
• Primary Citation of Related Structures:  
  4JV7, 4JV9, 4JVE, 4JVR, 4JWR


• PubMed Abstract: 
  

Structural analysis of both the MDM2-p53 protein-protein interaction and several small molecules bound to MDM2 led to the design and synthesis of tetrasubstituted morpholinone 10, an MDM2 inhibitor with a biochemical IC50 of 1.0 μM. The cocrystal structure of 10 with MDM2 inspired two independent optimization strategies and resulted in the discovery of morpholinones 16 and 27 possessing distinct binding modes. Both analogues were potent MDM2 inhibitors in biochemical and cellular assays, and morpholinone 27 (IC50 = 0.10 μM) also displayed suitable PK profile for in vivo animal experiments. A pharmacodynamic (PD) experiment in mice implanted with human SJSA-1 tumors showed p21(WAF1) mRNA induction (2.7-fold over vehicle) upon oral dosing of 27 at 300 mg/kg.

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Organizational Affiliation: 

Department of Therapeutic Discovery, Amgen Inc. , 1120 Veterans Boulevard, South San Francisco, California 94080, USA.

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: 11.77 kDa 
• Atom Count: 793 
• Modelled Residue Count: 85 
• 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1MN	B [auth A]	(2S,5R,6S)-2-benzyl-5,6-bis(4-bromophenyl)-4-methylmorpholin-3-one C24 H21 Br2 N O2 YYVYIVSNIAMIER-ZRBLBEILSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
1MN	PDBBind:  4JV7	IC50: 1000 (nM) from 1 assay(s)
	BindingDB:  4JV7	IC50: min: 1000, max: 3.00e+4 (nM) from 3 assay(s)
	Binding MOAD:  4JV7	IC50: 1000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.281 
• R-Value Work: 0.230 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.846	α = 90
b = 59.846	β = 90
c = 75.275	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: 2013-05-01 
Deposition Author(s): Huang, X., Gonzalez-Lopez de Turiso, F., Sun, D., Yosup, R., Bartberger, M.D., Beck, H.P., Cannon, J., Shaffer, P., Oliner, J.D., Olson, S.H., Medina, J.C.

Revision History  

• Version 1.0: 2013-05-01
  Type: Initial release
  
• Version 1.1: 2013-06-05
  Changes: Database references