The 1.6A Crystal Structure of Humanized Xenopus MDM2 with RO5027344

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 

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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: https://doi.org/10.1016/j.bmc.2014.05.072
  • Primary Citation of Related Structures:  
    4LWT, 4LWU

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm286Xenopus laevisMutation(s): 3 
Gene Names: mdm2
EC: 6.3.2
Find proteins for P56273 (Xenopus laevis)
Explore P56273 
Go to UniProtKB:  P56273
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56273
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 20Q

Download Ideal Coordinates CCD File 
B [auth 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
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
20Q Binding MOAD:  4LWT IC50: 3900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.066α = 90
b = 67.976β = 90
c = 67.168γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations