The 1.25A crystal structure of humanized Xenopus MDM2 with a nutlin fragment, RO5045331

Experimental Data Snapshot

  • Resolution: 1.25 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

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Deconstruction of a nutlin: dissecting the binding determinants of a potent protein-protein interaction inhibitor.

Fry, D.C.Wartchow, C.Graves, B.Janson, C.Lukacs, C.Kammlott, U.Belunis, C.Palme, S.Klein, C.Vu, B.

(2013) ACS Med Chem Lett 4: 660-665

  • DOI: https://doi.org/10.1021/ml400062c
  • Primary Citation of Related Structures:  
    4J74, 4J7D, 4J7E

  • PubMed Abstract: 

    Protein-protein interaction (PPI) systems represent a rich potential source of targets for drug discovery, but historically have proven to be difficult, particularly in the lead identification stage. Application of the fragment-based approach may help toward success with this target class. To provide an example toward understanding the potential issues associated with such an application, we have deconstructed one of the best established protein-protein inhibitors, the Nutlin series that inhibits the interaction between MDM2 and p53, into fragments, and surveyed the resulting binding properties using heteronuclear single quantum coherence nuclear magnetic resonance (HSQC NMR), surface plasmon resonance (SPR), and X-ray crystallography. We report the relative contributions toward binding affinity for each of the key substituents of the Nutlin molecule and show that this series could hypothetically have been discovered via a fragment approach. We find that the smallest fragment of Nutlin that retains binding accesses two subpockets of MDM2 and has a molecular weight at the high end of the range that normally defines fragments.

  • Organizational Affiliation

    Roche Research Center , 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 I31

Download Ideal Coordinates CCD File 
B [auth A](4S,5R)-2-(4-tert-butyl-2-ethoxyphenyl)-4,5-bis(4-chlorophenyl)-4,5-dimethyl-4,5-dihydro-1H-imidazole
C29 H32 Cl2 N2 O
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
I31 PDBBind:  4J7D Kd: 2.00e+4 (nM) from 1 assay(s)
Binding MOAD:  4J7D Kd: 2.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.25 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.639α = 90
b = 38.158β = 90
c = 69.027γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data 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: 2013-08-07
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations