Crystal structure of human mdm2 with a dihydroimidazothiazole inhibitor

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Synthesis and evaluation of novel orally active p53-MDM2 interaction inhibitors

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

(2013) Bioorg Med Chem 21: 4319-4331

  • DOI: https://doi.org/10.1016/j.bmc.2013.04.056
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We have discovered and reported potent p53-MDM2 interaction inhibitors possessing dihydroimidazothiazole scaffold. Our lead showed strong activity in vitro, but did not exhibit antitumor efficacy in vivo for the low metabolic stability. In order to obtain orally active compounds, we executed further optimization of our lead by the improvement of physicochemical properties. Thus we furnished optimal compounds by introducing an alkyl group onto the pyrrolidine at the C-2 substituent to prevent the metabolism; and modifying the terminal substituent of the proline motif improved solubility. These optimal compounds exhibited good PK profiles and significant antitumor efficacy with oral administration on a xenograft model using MV4-11 cells having wild type p53.

  • Organizational Affiliation

    Medicinal Chemistry Research Laboratories, R&D Division, Daiichi Sankyo Co., Ltd, 1-2-58 Hiromachi, Shinagawa-ku, 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
PHAROS:  Q00987
GTEx:  ENSG00000135679 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00987
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on LTZ

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
C36 H43 Cl2 N5 O3 S
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B],
G [auth B]
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
LTZ PDBBind:  3W69 IC50: 58 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.562α = 90
b = 65.761β = 90
c = 81.436γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PROCESSdata 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: 2013-06-05
    Type: Initial release
  • Version 1.1: 2014-04-30
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description