3KJD

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

• PDB DOI: https://doi.org/10.2210/pdb3KJD/pdb

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


• Deposited: 2009-11-03 Released: 2009-11-17 
• Deposition Author(s): Karlberg, T., Schutz, P., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Kallas, A., Kotenyova, T., Kotzsch, A., Kraulis, P., Nielsen, T.K., Moche, M., Nordlund, P., Nyman, T., Persson, C., Roos, A.K., Siponen, M.I., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Schuler, H., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.232 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 

Starting Model: experimental

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

• PubMed: 20092359 
• DOI: https://doi.org/10.1021/bi902079y
• Primary Citation of Related Structures:  
  3KCZ, 3KJD


• 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 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.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 84.33 kDa 
• Atom Count: 6,105 
• Modelled Residue Count: 702 
• Deposited Residue Count: 736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase 2	A, B	368	Homo sapiens	Mutation(s): 0  Gene Names: ADPRT2, ADPRTL2, PARP2 EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGN5 (Homo sapiens) Explore Q9UGN5  Go to UniProtKB:  Q9UGN5
PHAROS:  Q9UGN5 GTEx:  ENSG00000129484

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
78P	C [auth A], E [auth B]	(2R)-2-(7-carbamoyl-1H-benzimidazol-2-yl)-2-methylpyrrolidinium C13 H16 N4 O JNAHVYVRKWKWKQ-CYBMUJFWSA-N
GOL	D [auth A], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
78P	BindingDB:  3KJD	Kd: 5.8 (nM) from 1 assay(s)
		IC50: min: 1.3, max: 138 (nM) from 8 assay(s)
	PDBBind:  3KJD	Kd: 2.9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.232 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.134	α = 90
b = 134.611	β = 117.68
c = 58.314	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-17 
Deposition Author(s): Karlberg, T., Schutz, P., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Kallas, A., Kotenyova, T., Kotzsch, A., Kraulis, P., Nielsen, T.K., Moche, M., Nordlund, P., Nyman, T., Persson, C., Roos, A.K., Siponen, M.I., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Schuler, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary