5O2D

PARP14 Macrodomain 2 with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of a Selective Allosteric Inhibitor Targeting Macrodomain 2 of Polyadenosine-Diphosphate-Ribose Polymerase 14.

Schuller, M.Riedel, K.Gibbs-Seymour, I.Uth, K.Sieg, C.Gehring, A.P.Ahel, I.Bracher, F.Kessler, B.M.Elkins, J.M.Knapp, S.

(2017) ACS Chem Biol 12: 2866-2874

  • DOI: https://doi.org/10.1021/acschembio.7b00445
  • Primary Citation of Related Structures:  
    5O2D

  • PubMed Abstract: 

    Macrodomains are conserved protein interaction modules that can be found in all domains of life including in certain viruses. Macrodomains mediate recognition of sequence motifs harboring adenosine diphosphate ribose (ADPR) modifications, thereby regulating a variety of cellular processes. Due to their role in cancer or viral pathogenesis, macrodomains have emerged as potential therapeutic targets, but the unavailability of small molecule inhibitors has hampered target validation studies so far. Here, we describe an efficient screening strategy for identification of small molecule inhibitors that displace ADPR from macrodomains. We report the discovery and characterization of a macrodomain inhibitor, GeA-69, selectively targeting macrodomain 2 (MD2) of PARP14 with low micromolar affinity. Co-crystallization of a GeA-69 analogue with PARP14 MD2 revealed an allosteric binding mechanism explaining its selectivity over other human macrodomains. We show that GeA-69 engages PARP14 MD2 in intact cells and prevents its localization to sites of DNA damage.


  • Organizational Affiliation

    Structural Genomics Consortium (SGC), Nuffield Department of Clinical Medicine, University of Oxford , Oxford, OX3 7DQ, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 14200Homo sapiensMutation(s): 4 
Gene Names: PARP14BAL2KIAA1268
EC: 2.4.2.30
UniProt & NIH Common Fund Data Resources
Find proteins for Q460N5 (Homo sapiens)
Explore Q460N5 
Go to UniProtKB:  Q460N5
PHAROS:  Q460N5
GTEx:  ENSG00000173193 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ460N5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9HH
Query on 9HH

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[2-(9~{H}-carbazol-1-yl)phenyl]methanesulfonamide
C19 H16 N2 O2 S
FKXDARRJLQDNOV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
9HH BindingDB:  5O2D Kd: 2100 (nM) from 1 assay(s)
IC50: 900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.408α = 90
b = 35.74β = 94.83
c = 37.15γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-08
    Type: Initial release
  • Version 1.1: 2017-11-29
    Changes: Database references
  • Version 1.2: 2018-02-21
    Changes: Structure summary
  • Version 1.3: 2018-09-19
    Changes: Data collection, Database references