The 1.9A crystal structure of humanized Xenopus Mdm2 with nutlin-3a

Experimental Data Snapshot

  • Resolution: 1.91 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

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This is version 1.2 of the entry. See complete history


Discovery of RG7112: A Small-Molecule MDM2 Inhibitor in Clinical Development.

Vu, B.Wovkulich, P.Pizzolato, G.Lovey, A.Ding, Q.Jiang, N.Liu, J.J.Zhao, C.Glenn, K.Wen, Y.Tovar, C.Packman, K.Vassilev, L.Graves, B.

(2013) ACS Med Chem Lett 4: 466-469

  • DOI: https://doi.org/10.1021/ml4000657
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The p53 tumor suppressor is a potent transcription factor that plays a key role in the regulation of cellular responses to stress. It is controlled by its negative regulator MDM2, which binds directly to p53 and inhibits its transcriptional activity. MDM2 also targets p53 for degradation by the proteasome. Many tumors produce high levels of MDM2, thereby impairing p53 function. Restoration of p53 activity by inhibiting the p53-MDM2 interaction may represent a novel approach to cancer treatment. RG7112 (2g) is the first clinical small-molecule MDM2 inhibitor designed to occupy the p53-binding pocket of MDM2. In cancer cells expressing wild-type p53, RG7112 stabilizes p53 and activates the p53 pathway, leading to cell cycle arrest, apoptosis, and inhibition or regression of human tumor xenografts.

  • Organizational Affiliation

    Discovery Chemistry, Discovery Oncology, Discovery Technologies, 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 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 NUT

Download Ideal Coordinates CCD File 
B [auth A]4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one
C30 H30 Cl2 N4 O4
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
NUT PDBBind:  4J3E IC50: 88 (nM) from 1 assay(s)
Binding MOAD:  4J3E IC50: 88 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.91 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.887α = 90
b = 67.657β = 90
c = 67.173γ = 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: 2013-04-24
    Type: Initial release
  • Version 1.1: 2014-10-08
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations