Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.75 kDa 
• Atom Count: 3456 
• Modelled Residue Count: 380 
• Deposited Residue Count: 382 
• Unique protein chains: 1

5LX6

Human PARP10 (ARTD10), catalytic fragment in complex with PARP inhibitor Veliparib

• PDB DOI: 10.2210/pdb5LX6/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-20 Released: 2017-01-11 
• Deposition Author(s): Karlberg, T., Thorsell, A.G., Schuler, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.213 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

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

• PubMed: 28001384 
• DOI: 10.1021/acs.jmedchem.6b00990
• Primary Citation of Related Structures:  
  4R5W, 4R6E, 4RV6, 4TVJ, 4UND, 4UXB, 5LX6


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase 10	A, B	191	Homo sapiens	Mutation(s): 0  Gene Names: PARP10 EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q53GL7 (Homo sapiens) Explore Q53GL7  Go to UniProtKB:  Q53GL7
PHAROS:  Q53GL7 GTEx:  ENSG00000178685

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
78P	C [auth A], D [auth B]	(2R)-2-(7-carbamoyl-1H-benzimidazol-2-yl)-2-methylpyrrolidinium C13 H16 N4 O JNAHVYVRKWKWKQ-CYBMUJFWSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
78P	BindingDB:  5LX6	IC50: min: 1900, max: 4.38e+4 (nM) from 4 assay(s)
	Binding MOAD:  5LX6	IC50: 1900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.213 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.48	α = 90
b = 88.677	β = 104.68
c = 58.405	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-09-20 
• Released Date: 2017-01-11 
Deposition Author(s): Karlberg, T., Thorsell, A.G., Schuler, H.

Revision History  

• Version 1.0: 2017-01-11
  Type: Initial release
  
• Version 1.1: 2017-03-08
  Changes: Database references