6HMN

POLYADPRIBOSYL GLYCOSIDASE IN COMPLEX WITH PDD00014909


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cell-Active Small Molecule Inhibitors of the DNA-Damage Repair Enzyme Poly(ADP-ribose) Glycohydrolase (PARG): Discovery and Optimization of Orally Bioavailable Quinazolinedione Sulfonamides.

Waszkowycz, B.Smith, K.M.McGonagle, A.E.Jordan, A.M.Acton, B.Fairweather, E.E.Griffiths, L.A.Hamilton, N.M.Hamilton, N.S.Hitchin, J.R.Hutton, C.P.James, D.I.Jones, C.D.Jones, S.Mould, D.P.Small, H.F.Stowell, A.I.J.Tucker, J.A.Waddell, I.D.Ogilvie, D.J.

(2018) J.Med.Chem. 61: 10767-10792

  • DOI: 10.1021/acs.jmedchem.8b01407
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA damage repair enzymes are promising targets in the development of new therapeutic agents for a wide range of cancers and potentially other diseases. The enzyme poly(ADP-ribose) glycohydrolase (PARG) plays a pivotal role in the regulation of DNA r ...

    DNA damage repair enzymes are promising targets in the development of new therapeutic agents for a wide range of cancers and potentially other diseases. The enzyme poly(ADP-ribose) glycohydrolase (PARG) plays a pivotal role in the regulation of DNA repair mechanisms; however, the lack of potent drug-like inhibitors for use in cellular and in vivo models has limited the investigation of its potential as a novel therapeutic target. Using the crystal structure of human PARG in complex with the weakly active and cytotoxic anthraquinone 8a, novel quinazolinedione sulfonamides PARG inhibitors have been identified by means of structure-based virtual screening and library design. 1-Oxetan-3-ylmethyl derivatives 33d and 35d were selected for preliminary investigations in vivo. X-ray crystal structures help rationalize the observed structure-activity relationships of these novel inhibitors.


    Organizational Affiliation

    Cancer Research UK Manchester Institute , The University of Manchester , Alderley Park , Maccelsfield SK10 4TG , U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poly(ADP-ribose) glycohydrolase
A
531Homo 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
70J
Query on 70J

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Download CCD File 
A
3-methyl-6-[[(1-methylcyclopropyl)amino]-bis(oxidanyl)-$l^{4}-sulfanyl]-1-(phenylmethyl)quinazoline-2,4-dione
C20 H23 N3 O4 S
WQSNZLBPHUSAAJ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.330α = 90.00
b = 89.630β = 90.00
c = 96.250γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2018-11-21
    Type: Data collection, Database references
  • Version 1.2: 2019-04-24
    Type: Data collection, Database references