6EK3

PARP15 CATALYTIC DOMAIN MUTANT (Y598L) IN COMPLEX WITH OUL35


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

4-(Phenoxy) and 4-(benzyloxy)benzamides as potent and selective inhibitors of mono-ADP-ribosyltransferase PARP10/ARTD10.

Murthy, S.Desantis, J.Verheugd, P.Maksimainen, M.M.Venkannagari, H.Massari, S.Ashok, Y.Obaji, E.Nkizinkinko, Y.Luscher, B.Tabarrini, O.Lehtio, L.

(2018) Eur J Med Chem 156: 93-102

  • DOI: https://doi.org/10.1016/j.ejmech.2018.06.047
  • Primary Citation of Related Structures:  
    6EK3

  • PubMed Abstract: 

    Human Diphtheria toxin-like ADP-ribosyltranferases (ARTD) 10 is an enzyme carrying out mono-ADP-ribosylation of a range of cellular proteins and affecting their activities. It shuttles between cytoplasm and nucleus and influences signaling events in both compartments, such as nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling and S phase DNA repair. Furthermore, overexpression of ARTD10 induces cell death. We recently reported on the discovery of a hit compound, OUL35 (compound 1), with 330 nM potency and remarkable selectivity towards ARTD10 over other enzymes in the human protein family. Here we aimed at establishing a structure-activity relationship of the OUL35 scaffold, by evaluating an array of 4-phenoxybenzamide derivatives. By exploring modifications on the linker between the aromatic rings, we identified also a 4-(benzyloxy)benzamide derivative, compound 32, which is potent (IC 50  = 230 nM) and selective, and like OUL35 was able to rescue HeLa cells from ARTD10-induced cell death. Evaluation of an enlarged series of derivatives produced detailed knowledge on the structural requirements for ARTD10 inhibition and allowed the discovery of further tool compounds with submicromolar cellular potency that will help in understanding the roles of ARTD10 in biological systems.


  • Organizational Affiliation

    Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 15
A, B
221Homo sapiensMutation(s): 1 
Gene Names: PARP15BAL3
EC: 2.4.2.30
UniProt & NIH Common Fund Data Resources
Find proteins for Q460N3 (Homo sapiens)
Explore Q460N3 
Go to UniProtKB:  Q460N3
PHAROS:  Q460N3
GTEx:  ENSG00000173200 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ460N3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OUL
Query on OUL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
4-(4-aminocarbonylphenoxy)benzamide
C14 H12 N2 O3
XZRCQWLPMXFGHE-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
OUL BindingDB:  6EK3 IC50: min: 295, max: 1.00e+4 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.2α = 90
b = 68.89β = 90
c = 161.43γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland287063
Academy of FinlandFinland294085

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description