3KJD

Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor ABT-888


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the catalytic domain of human PARP2 in complex with PARP inhibitor ABT-888.

Karlberg, T.Hammarstrom, M.Schutz, P.Svensson, L.Schuler, H.

(2010) Biochemistry 49: 1056-1058

  • DOI: 10.1021/bi902079y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Poly-ADP-ribose polymerases (PARPs) catalyze transfer of ADP-ribose from NAD(+) to specific residues in their substrate proteins or to growing ADP-ribose chains. PARP activity is involved in processes such as chromatin remodeling, transcription contr ...

    Poly-ADP-ribose polymerases (PARPs) catalyze transfer of ADP-ribose from NAD(+) to specific residues in their substrate proteins or to growing ADP-ribose chains. PARP activity is involved in processes such as chromatin remodeling, transcription control, and DNA repair. Inhibitors of PARP activity may be useful in cancer therapy. PARP2 is the family member that is most similar to PARP1, and the two can act together as heterodimers. We used X-ray crystallography to determine two structures of the catalytic domain of human PARP2: the complexes with PARP inhibitors 3-aminobenzamide and ABT-888. These results contribute to our understanding of structural features and compound properties that can be employed to develop selective inhibitors of human ADP-ribosyltransferases.


    Organizational Affiliation

    Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles vag 2, 17177 Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poly [ADP-ribose] polymerase 2
A, B
368Homo sapiensMutation(s): 0 
Gene 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
78P
Query on 78P

Download SDF File 
Download CCD File 
A, B
(2R)-2-(7-carbamoyl-1H-benzimidazol-2-yl)-2-methylpyrrolidinium
C13 H16 N4 O
JNAHVYVRKWKWKQ-CYBMUJFWSA-N
 Ligand Interaction
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
78PKd: 5.8 nM (99) BINDINGDB
78PKd: 2.9 nM BINDINGMOAD
78PKd: 2.9 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.134α = 90.00
b = 134.611β = 117.68
c = 58.314γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DNAdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance