The 1.14A Crystal Structure of Humanized Xenopus MDM2 with RO5499252

Experimental Data Snapshot

  • Resolution: 1.14 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

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This is version 1.2 of the entry. See complete history


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 Mdm285Xenopus 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 20U

Download Ideal Coordinates CCD File 
B [auth A](2'S,3R,4'S,5'R)-N-(4-carbamoylphenyl)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide
C30 H29 Cl2 F N4 O3
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
20U Binding MOAD:  4LWU IC50: 5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.14 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.554α = 90
b = 78.341β = 90
c = 24.703γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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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