The 1.9A crystal structure of humanized Xenopus MDM2 with RO5313109 - a pyrrolidine MDM2 inhibitor

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 

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Ligand Structure Quality Assessment 

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Discovery of RG7388, a Potent and Selective p53-MDM2 Inhibitor in Clinical Development.

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

(2013) J Med Chem 56: 5979-5983

  • DOI: https://doi.org/10.1021/jm400487c
  • Primary Citation of Related Structures:  
    4JRG, 4JSC

  • PubMed Abstract: 

    Restoration of p53 activity by inhibition of the p53-MDM2 interaction has been considered an attractive approach for cancer treatment. However, the hydrophobic protein-protein interaction surface represents a significant challenge for the development of small-molecule inhibitors with desirable pharmacological profiles. RG7112 was the first small-molecule p53-MDM2 inhibitor in clinical development. Here, we report the discovery and characterization of a second generation clinical MDM2 inhibitor, RG7388, with superior potency and selectivity.

  • Organizational Affiliation

    Discovery Chemistry, ‡Discovery Technologies, §Discovery Oncology, ∥Non-Clinical Development, Roche Research Center, Hoffmann-La Roche, Inc. , 340 Kingsland Street, Nutley, New Jersey 07110, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2
A, B
85Xenopus 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on I09

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C27 H33 Cl2 N3 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
I09 PDBBind:  4JRG IC50: 196 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.542α = 90
b = 72.796β = 111.78
c = 43.865γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
d*TREKdata 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: 2013-07-24
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations