3VZV

Crystal structure of human mdm2 with a dihydroimidazothiazole inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

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: 10.1016/j.bmcl.2012.11.091

  • 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 b ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase Mdm2
A, B
87Homo sapiensMutation(s): 1 
Gene Names: MDM2
EC: 2.3.2.27
Find proteins for Q00987 (Homo sapiens)
Go to Gene View: MDM2
Go to UniProtKB:  Q00987
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VZV
Query on VZV
Download SDF File 
Download CCD File 
A, B
1-{[(5R,6S)-5,6-bis(4-chlorophenyl)-6-methyl-3-(propan-2-yl)-5,6-dihydroimidazo[2,1-b][1,3]thiazol-2-yl]carbonyl}-N,N-dimethyl-L-prolinamide
C29 H32 Cl2 N4 O2 S
BWUMOCARMRPCIP-HQQGYVGFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VZVIC50: 9.2 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.255α = 90.00
b = 66.076β = 90.00
c = 80.419γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-06
    Type: Initial release