6OA3

Structure of human PARG complexed with JA2131


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

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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:  
    6O9Y, 6O9X, 6OA1, 6OA0, 6OA3, 6OAK, 6OAL

  • 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 resistance to PARP1 inhibitors ...

    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

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poly(ADP-ribose) glycohydrolaseA533Homo sapiensMutation(s): 6 
Gene Names: PARG
EC: 3.2.1.143
UniProt & NIH Common Fund Data Resources
Find proteins for Q86W56 (Homo sapiens)
Explore Q86W56 
Go to UniProtKB:  Q86W56
PHAROS:  Q86W56
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M0M (Subject of Investigation/LOI)
Query on M0M

Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
M0M Binding MOAD:  6OA3 IC50: 400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.675α = 90
b = 65.948β = 95.44
c = 88.598γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

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