Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 21.55 kDa 
• Atom Count: 1490 
• Modelled Residue Count: 170 
• Deposited Residue Count: 174 
• Unique protein chains: 1

3VZV

Crystal structure of human mdm2 with a dihydroimidazothiazole inhibitor

• PDB DOI: 10.2210/pdb3VZV/pdb

• Classification: LIGASE/LIGASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-10-16 Released: 2013-02-06 
• Deposition Author(s): Shimizu, H., Katakura, S., Miyazaki, M., Naito, H., Sugimoto, Y., Kawato, H., Okayama, T., Soga, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.284 
• R-Value Work: 0.248 
• R-Value Observed: 0.250 

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

• PubMed: 23266121 
• DOI: 10.1016/j.bmcl.2012.11.091
• Primary Citation of Related Structures:  
  3VZV


• 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.

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Organizational Affiliation: 

Lead Discovery & Optimization Research Laboratories II, R&D Division, Daiichi Sankyo Co., Ltd, 1-2-58 Hiromachi, Tokyo 140-8710, Japan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A, B	87	Homo sapiens	Mutation(s): 1  Gene Names: MDM2 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens) Explore Q00987  Go to UniProtKB:  Q00987
PHAROS:  Q00987

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VZV	C [auth A], D [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
VZV	PDBBind:  3VZV	IC50: 9.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 58.255	α = 90
b = 66.076	β = 90
c = 80.419	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-16 
• Released Date: 2013-02-06 
Deposition Author(s): Shimizu, H., Katakura, S., Miyazaki, M., Naito, H., Sugimoto, Y., Kawato, H., Okayama, T., Soga, T.

Revision History  

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