6AFJ

DJ-1 with compound 13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.

Tashiro, S.Caaveiro, J.M.M.Nakakido, M.Tanabe, A.Nagatoishi, S.Tamura, Y.Matsuda, N.Liu, D.Hoang, Q.Q.Tsumoto, K.

(2018) ACS Chem. Biol. 13: 2783-2793

  • DOI: 10.1021/acschembio.8b00701
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DJ-1 is a Parkinson's disease associated protein endowed with enzymatic, redox sensing, regulatory, chaperoning, and neuroprotective activities. Although DJ-1 has been vigorously studied for the past decade and a half, its exact role in the progressi ...

    DJ-1 is a Parkinson's disease associated protein endowed with enzymatic, redox sensing, regulatory, chaperoning, and neuroprotective activities. Although DJ-1 has been vigorously studied for the past decade and a half, its exact role in the progression of the disease remains uncertain. In addition, little is known about the spatiotemporal regulation of DJ-1, or the biochemical basis explaining its numerous biological functions. Progress has been hampered by the lack of inhibitors with precisely known mechanisms of action. Herein, we have employed biophysical methodologies and X-ray crystallography to identify and to optimize a family of compounds inactivating the critical Cys106 residue of human DJ-1. We demonstrate these compounds are potent inhibitors of various activities of DJ-1 in vitro and in cell-based assays. This study reports a new family of DJ-1 inhibitors with a defined mechanism of action, and contributes toward the understanding of the biological function of DJ-1.


    Related Citations: 
    • Thermodynamic and structural characterization of the specific binding of Zn(II) to human protein DJ-1.
      Tashiro, S.,Caaveiro, J.M.M.,Wu, C.X.,Hoang, Q.Q.,Tsumoto, K.
      (2014) Biochemistry 53: 2218


    Organizational Affiliation

    Institute of Medical Science , The University of Tokyo , Tokyo 108-8639 , Japan.,Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science , 2-1-6 Kamikitazawa , Setagaya, Tokyo 156-8506 , Japan.,Laboratory of Global Healthcare, Graduate School of Pharmaceutical Sciences , Kyushu University , Fukuoka 812-8582 , Japan.,Department of Chemistry and Biotechnology, School of Engineering , The University of Tokyo , Tokyo 108-8639 , Japan.,Department of Material and Biological Chemistry, Faculty of Science , Yamagata University , Yamagata 990-8560 , Japan.,Department of Chemistry and Biochemistry , Loyola University Chicago , Chicago , Illinois 60660 , United States.,Department of Bioengineering, Graduate School of Engineering , The University of Tokyo , Tokyo 113-8656 , Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein/nucleic acid deglycase DJ-1
A
189Homo sapiensMutation(s): 0 
Gene Names: PARK7
EC: 3.1.2.-, 3.5.1.-, 3.5.1.124
Find proteins for Q99497 (Homo sapiens)
Go to Gene View: PARK7
Go to UniProtKB:  Q99497
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
73G
Query on 73G

Download SDF File 
Download CCD File 
A
butyl 2-[2,3-bis(oxidanylidene)indol-1-yl]ethanoate
C14 H15 N O4
KSZFFJNYVZVNIQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.139 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 75.140α = 90.00
b = 75.140β = 90.00
c = 75.910γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanPlatform for Drug Discovery, Informatics and Structural Life Science
Japan Society for the Promotion of ScienceJapan25249115
Japan Society for the Promotion of ScienceJapan16H02420
Japan Society for the Promotion of ScienceJapan15K06962

Revision History 

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-10-03
    Type: Data collection, Database references