4LWT

The 1.6A Crystal Structure of Humanized Xenopus MDM2 with RO5027344


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of potent and selective spiroindolinone MDM2 inhibitor, RO8994, for cancer therapy.

Zhang, Z.Ding, Q.Liu, J.J.Zhang, J.Jiang, N.Chu, X.J.Bartkovitz, D.Luk, K.C.Janson, C.Tovar, C.Filipovic, Z.M.Higgins, B.Glenn, K.Packman, K.Vassilev, L.T.Graves, B.

(2014) Bioorg.Med.Chem. 22: 4001-4009

  • DOI: 10.1016/j.bmc.2014.05.072
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The field of small-molecule inhibitors of protein-protein interactions is rapidly advancing and the specific area of inhibitors of the p53/MDM2 interaction is a prime example. Several groups have published on this topic and multiple compounds are in ...

    The field of small-molecule inhibitors of protein-protein interactions is rapidly advancing and the specific area of inhibitors of the p53/MDM2 interaction is a prime example. Several groups have published on this topic and multiple compounds are in various stages of clinical development. Building on the strength of the discovery of RG7112, a Nutlin imidazoline-based compound, and RG7388, a pyrrolidine-based compound, we have developed additional scaffolds that provide opportunities for future development. Here, we report the discovery and optimization of a highly potent and selective series of spiroindolinone small-molecule MDM2 inhibitors, culminating in RO8994.


    Organizational Affiliation

    Discovery Chemistry, Roche Research Center, Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07110, United States. Electronic address: zzhang85@its.jnj.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase Mdm2
A
86Xenopus laevisMutation(s): 3 
Gene Names: mdm2
EC: 2.3.2.27
Find proteins for P56273 (Xenopus laevis)
Go to UniProtKB:  P56273
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
20Q
Query on 20Q

Download SDF File 
Download CCD File 
A
(3S)-3-[(3R)-1-acetylpiperidin-3-yl]-6-chloro-3-(3-chlorobenzyl)-1,3-dihydro-2H-indol-2-one
C22 H22 Cl2 N2 O2
RIBYLXUNNWIWJK-AOMKIAJQSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
20QIC50: 3900 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.222 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 43.066α = 90.00
b = 67.976β = 90.00
c = 67.168γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling
CNXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-08-13
    Type: Database references