4JV7

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

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

  • DOI: 10.1021/jm400293z
  • Primary Citation of Related Structures:  

  • 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 str ...

    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.

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase Mdm2
A
96Homo sapiensMutation(s): 0 
Gene Names: MDM2
EC: 2.3.2.27
Find proteins for Q00987 (Homo sapiens)
Go to Gene View: MDM2
Go to UniProtKB:  Q00987
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
1MN
Query on 1MN
Download SDF File 
Download CCD File 
A
(2S,5R,6S)-2-benzyl-5,6-bis(4-bromophenyl)-4-methylmorpholin-3-one
C24 H21 Br2 N O2
YYVYIVSNIAMIER-ZRBLBEILSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1MNIC50: 1000 - >30000 nM (100) BINDINGDB
1MNIC50: 1000 nM BINDINGMOAD
1MNIC50: 1000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.230 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.846α = 90.00
b = 59.846β = 90.00
c = 75.275γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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