Crystal structure of human mdm2 with a dihydroimidazothiazole inhibitor

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 

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Lead optimization of novel p53-MDM2 interaction inhibitors possessing dihydroimidazothiazole scaffold

Miyazaki, M.Naito, H.Sugimoto, Y.Kawato, H.Okayama, T.Shimizu, H.Miyazaki, M.Kitagawa, M.Seki, T.Fukutake, S.Aonuma, M.Soga, T.

(2013) Bioorg Med Chem Lett 23: 728-732

  • DOI: https://doi.org/10.1016/j.bmcl.2012.11.091
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    With the aim of discovering potent inhibitors of the p53-MDM2 interaction and thus obtaining a potent anticancer drug, we have pursued synthesis and optimization of dihydroimidazothiazole derivatives, which have been discovered via scaffold hopping by mimicing the mode of interaction between MDM2 and Nutlins. Upon the discovery we encountered a problem involving the chemical instability of the scaffold, that is, susceptibility to oxidation which led to imidazothiazole. In order to solve this problem and to obtain further potent compounds, we executed medicinal research and thus furnished the optimal compounds by incorporating the methyl group onto the C-6 position to avoid the oxidation, and by modifying the C-2 moiety of the additional proline motif, which furnished high potency. The incorporation of the pyrrolidine moiety at the C-2 position raised another hydrophobic interaction site with MDM2 protein, which was generated by the induced-fitting observed by co-crystal structure analysis. These optimal molecules showed significant improvement in potency when compared with the early lead (+)-1 or Nutlin-3a.

  • Organizational Affiliation

    Lead Discovery & Optimization Research Laboratories II, R&D Division, Daiichi Sankyo Co., Ltd, 1-2-58 Hiromachi, Tokyo 140-8710, Japan. miyazaki.masaki.p3@daiichisankyo.co.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2
A, B
87Homo sapiensMutation(s): 1 
Gene Names: MDM2
EC: 6.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens)
Explore Q00987 
Go to UniProtKB:  Q00987
GTEx:  ENSG00000135679 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00987
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on VZV

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C29 H32 Cl2 N4 O2 S
Binding Affinity Annotations 
IDSourceBinding Affinity
VZV PDBBind:  3VZV IC50: 9.2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.255α = 90
b = 66.076β = 90
c = 80.419γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data 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: 2013-02-06
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations