4F1Q

Human Artd8 (Parp14, Bal2) - catalytic domain in complex with A16(E)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Ligands for ADP-Ribosyltransferases via Docking-Based Virtual Screening.

Andersson, C.D.Karlberg, T.Ekblad, T.Lindgren, A.E.Thorsell, A.G.Spjut, S.Uciechowska, U.Niemiec, M.S.Wittung-Stafshede, P.Weigelt, J.Elofsson, M.Schuler, H.Linusson, A.

(2012) J.Med.Chem. 55: 7706-7718

  • DOI: 10.1021/jm300746d
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The diphtheria toxin-like ADP-ribosyltransferases (ARTDs) are an enzyme family that catalyzes the transfer of ADP-ribose units onto substrate proteins by using nicotinamide adenine dinucleotide (NAD(+)) as a cosubstrate. They have a documented role i ...

    The diphtheria toxin-like ADP-ribosyltransferases (ARTDs) are an enzyme family that catalyzes the transfer of ADP-ribose units onto substrate proteins by using nicotinamide adenine dinucleotide (NAD(+)) as a cosubstrate. They have a documented role in chromatin remodelling and DNA repair, and inhibitors of ARTD1 and 2 (PARP1 and 2) are currently in clinical trials for the treatment of cancer. The detailed function of most other ARTDs is still unknown. By using virtual screening, we identified small ligands of ARTD7 (PARP15/BAL3) and ARTD8 (PARP14/BAL2). Thermal-shift assays confirmed that 16 compounds, belonging to eight structural classes, bound to ARTD7/ARTD8. Affinity measurements with isothermal titration calorimetry for two isomers of the most promising hit compound confirmed binding in the low micromolar range to ARTD8. Crystal structures showed anchoring of the hits in the nicotinamide pocket. These results form a starting point in the development of chemical tools for the study of the role and function of ARTD7 and ARTD8.


    Organizational Affiliation

    Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poly [ADP-ribose] polymerase 14
A, B
193Homo sapiensMutation(s): 0 
Gene Names: PARP14 (BAL2, KIAA1268)
EC: 2.4.2.-
Find proteins for Q460N5 (Homo sapiens)
Go to Gene View: PARP14
Go to UniProtKB:  Q460N5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NO3
Query on NO3

Download SDF File 
Download CCD File 
B
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
0RZ
Query on 0RZ

Download SDF File 
Download CCD File 
A, B
(2E)-4-[(3-carbamoylphenyl)amino]-4-oxobut-2-enoic acid
C11 H10 N2 O4
GNFSYBNDPOBXLJ-SNAWJCMRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0RZIC50: >20000 nM (100) BINDINGDB
0RZKd: 11200 nM (100) BINDINGDB
0RZKd: 11200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.217 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 82.676α = 90.00
b = 144.986β = 90.00
c = 83.333γ = 90.00
Software Package:
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2012-09-26
    Type: Database references