4TVJ

HUMAN ARTD2 (PARP2) - CATALYTIC DOMAIN IN COMPLEX WITH OLAPARIB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for Potency and Promiscuity in Poly(ADP-ribose) Polymerase (PARP) and Tankyrase Inhibitors.

Thorsell, A.G.Ekblad, T.Karlberg, T.Low, M.Pinto, A.F.Tresaugues, L.Moche, M.Cohen, M.S.Schuler, H.

(2017) J. Med. Chem. 60: 1262-1271

  • DOI: 10.1021/acs.jmedchem.6b00990
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Selective inhibitors could help unveil the mechanisms by which inhibition of poly(ADP-ribose) polymerases (PARPs) elicits clinical benefits in cancer therapy. We profiled 10 clinical PARP inhibitors and commonly used research tools for their inhibiti ...

    Selective inhibitors could help unveil the mechanisms by which inhibition of poly(ADP-ribose) polymerases (PARPs) elicits clinical benefits in cancer therapy. We profiled 10 clinical PARP inhibitors and commonly used research tools for their inhibition of multiple PARP enzymes. We also determined crystal structures of these compounds bound to PARP1 or PARP2. Veliparib and niraparib are selective inhibitors of PARP1 and PARP2; olaparib, rucaparib, and talazoparib are more potent inhibitors of PARP1 but are less selective. PJ34 and UPF1069 are broad PARP inhibitors; PJ34 inserts a flexible moiety into hydrophobic subpockets in various ADP-ribosyltransferases. XAV939 is a promiscuous tankyrase inhibitor and a potent inhibitor of PARP1 in vitro and in cells, whereas IWR1 and AZ-6102 are tankyrase selective. Our biochemical and structural analysis of PARP inhibitor potencies establishes a molecular basis for either selectivity or promiscuity and provides a benchmark for experimental design in assessment of PARP inhibitor effects.


    Organizational Affiliation

    Program in Chemical Biology and Department of Physiology and Pharmacology, Health & Science University , Portland, Oregon 97210, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poly [ADP-ribose] polymerase 2
A, B
368Homo sapiensGene Names: PARP2 (ADPRT2, ADPRTL2)
EC: 2.4.2.30
Find proteins for Q9UGN5 (Homo sapiens)
Go to Gene View: PARP2
Go to UniProtKB:  Q9UGN5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
09L
Query on 09L

Download SDF File 
Download CCD File 
A, B
4-(3-{[4-(cyclopropylcarbonyl)piperazin-1-yl]carbonyl}-4-fluorobenzyl)phthalazin-1(2H)-one
Olaparib
C24 H23 F N4 O3
FDLYAMZZIXQODN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
09LIC50: 0.4 - 1 nM (99) BINDINGDB
09LKd: 0.3 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.083α = 90.00
b = 134.123β = 117.96
c = 58.348γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2017-01-18
    Type: Database references
  • Version 1.2: 2017-03-22
    Type: Database references