6OA3

Structure of human PARG complexed with JA2131


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Selective small molecule PARG inhibitor causes replication fork stalling and cancer cell death.

Houl, J.H.Ye, Z.Brosey, C.A.Balapiti-Modarage, L.P.F.Namjoshi, S.Bacolla, A.Laverty, D.Walker, B.L.Pourfarjam, Y.Warden, L.S.Babu Chinnam, N.Moiani, D.Stegeman, R.A.Chen, M.K.Hung, M.C.Nagel, Z.D.Ellenberger, T.Kim, I.K.Jones, D.E.Ahmed, Z.Tainer, J.A.

(2019) Nat Commun 10: 5654-5654

  • DOI: 10.1038/s41467-019-13508-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Poly(ADP-ribose)ylation (PARylation) by PAR polymerase 1 (PARP1) and PARylation removal by poly(ADP-ribose) glycohydrolase (PARG) critically regulate DNA damage responses; yet, conflicting reports obscure PARG biology and its impact on cancer cell re ...

    Poly(ADP-ribose)ylation (PARylation) by PAR polymerase 1 (PARP1) and PARylation removal by poly(ADP-ribose) glycohydrolase (PARG) critically regulate DNA damage responses; yet, conflicting reports obscure PARG biology and its impact on cancer cell resistance to PARP1 inhibitors. Here, we found that PARG expression is upregulated in many cancers. We employed chemical library screening to identify and optimize methylxanthine derivatives as selective bioavailable PARG inhibitors. Multiple crystal structures reveal how substituent positions on the methylxanthine core dictate binding modes and inducible-complementarity with a PARG-specific tyrosine clasp and arginine switch, supporting inhibitor specificity and a competitive inhibition mechanism. Cell-based assays show selective PARG inhibition and PARP1 hyperPARylation. Moreover, our PARG inhibitor sensitizes cells to radiation-induced DNA damage, suppresses replication fork progression and impedes cancer cell survival. In PARP inhibitor-resistant A172 glioblastoma cells, our PARG inhibitor shows comparable killing to Nedaplatin, providing further proof-of-concept that selectively inhibiting PARG can impair cancer cell survival.


    Organizational Affiliation

    Department of Pharmaceutical Sciences, The University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, AR, 72205, USA.,Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA. ZAhmed@mdanderson.org.,Department of Chemistry, University of Cincinnati, 301 Clifton Ct, Cincinnati, OH, 45221, USA. kimiw@ucmail.uc.edu.,Department of Chemistry, The University of Arkansas at Little Rock, 2801S. University Ave, Little Rock, AR, 72204, USA.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660S. Euclid Avenue, Saint Louis, MO, 63110, USA.,The University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660S. Euclid Avenue, Saint Louis, MO, 63110, USA. kimiw@ucmail.uc.edu.,Graduate Institute of Biomedical Sciences and Center for Molecular Medicine, and Office of the President, China Medical University, Taichung, 404, Taiwan.,Harvard University, School of Public Health, Boston, MA, 02115, USA.,Department of Chemistry, University of Cincinnati, 301 Clifton Ct, Cincinnati, OH, 45221, USA.,Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA. jtainer@mdanderson.org.,Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poly(ADP-ribose) glycohydrolase
A
533Homo sapiensMutation(s): 6 
Gene Names: PARG
EC: 3.2.1.143
Find proteins for Q86W56 (Homo sapiens)
Go to Gene View: PARG
Go to UniProtKB:  Q86W56
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M0M
Query on M0M

Download SDF File 
Download CCD File 
A
(8S)-1,3-dimethyl-8-{[2-(morpholin-4-yl)ethyl]sulfanyl}-6-sulfanylidene-1,3,6,7,8,9-hexahydro-2H-purin-2-one
C13 H21 N5 O2 S2
IDPRQIKRJXLJTP-LBPRGKRZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.675α = 90.00
b = 65.948β = 95.44
c = 88.598γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History 

  • Version 1.0: 2019-12-25
    Type: Initial release