7PA3

PARK7 with covalent inhibitor JYQ-88


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Chemical Toolkit for PARK7: Potent, Selective, and High-Throughput.

Jia, Y.Kim, R.Q.Kooij, R.Ovaa, H.Sapmaz, A.Geurink, P.P.

(2022) J Med Chem 65: 13288-13304

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01113
  • Primary Citation of Related Structures:  
    7PA2, 7PA3

  • PubMed Abstract: 

    The multifunctional human Parkinson's disease protein 7 (PARK7/DJ1) is an attractive therapeutic target due to its link with early-onset Parkinson's disease, upregulation in various cancers, and contribution to chemoresistance. However, only a few compounds have been identified to bind PARK7 due to the lack of a dedicated chemical toolbox. We report the creation of such a toolbox and showcase the application of each of its components. The selective PARK7 submicromolar inhibitor with a cyanimide reactive group covalently modifies the active site Cys106. Installment of different dyes onto the inhibitor delivered two PARK7 probes. The Rhodamine110 probe provides a high-throughput screening compatible FP assay, showcased by screening a compound library (8000 molecules). The SulfoCy5-equipped probe is a valuable tool to assess the effect of PARK7 inhibitors in a cell lysate. Our work creates new possibilities to explore PARK7 function in a physiologically relevant setting and develop new and improved PARK7 inhibitors.


  • Organizational Affiliation

    Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Parkinson disease protein 7A [auth AAA]192Homo sapiensMutation(s): 0 
Gene Names: PARK7
EC: 3.1.2 (PDB Primary Data), 3.5.1 (PDB Primary Data), 3.5.1.124 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q99497 (Homo sapiens)
Explore Q99497 
Go to UniProtKB:  Q99497
PHAROS:  Q99497
GTEx:  ENSG00000116288 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99497
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6SI (Subject of Investigation/LOI)
Query on 6SI

Download Ideal Coordinates CCD File 
B [auth AAA](3~{S})-~{N}-[5-[2-[(azanylidene-$l^{4}-azanylidene)amino]ethanoyl]-6,7-dihydro-4~{H}-[1,3]thiazolo[5,4-c]pyridin-2-yl]-1-(iminomethyl)pyrrolidine-3-carboxamide
C14 H23 N8 O2 S
SIHVOGFUBUCGRF-HVIDBACLSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.174 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.743α = 90
b = 66.743β = 90
c = 176.785γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 1.1: 2022-10-05
    Changes: Database references
  • Version 1.2: 2022-10-26
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description