3KR8

Human tankyrase 2 - catalytic PARP domain in complex with an inhibitor XAV939

• PDB DOI: https://doi.org/10.2210/pdb3KR8/pdb

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


• Deposited: 2009-11-18 Released: 2009-12-15 
• 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., Siponen, M.I., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Schuler, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.255 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 

Starting Model: experimental

Literature

Structural basis for the interaction between tankyrase-2 and a potent Wnt-signaling inhibitor.

Karlberg, T., Markova, N., Johansson, I., Hammarstrom, M., Schutz, P., Weigelt, J., Schuler, H.

(2010) J Med Chem 53: 5352-5355

• PubMed: 20565110 
• DOI: https://doi.org/10.1021/jm100249w
• Primary Citation of Related Structures:  
  3KR7, 3KR8


• PubMed Abstract: 
  

  We report two crystal structures of the PARP domain of human tankyrase-2 (TNKS2). Tankyrases are involved in fundamental cellular processes such as telomere homeostasis and Wnt signaling. The complex of TNKS2 with the potent inhibitor XAV939 provides insights into the molecular basis of the strong interaction and suggests routes for further development of tankyrase inhibitors.

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Organizational Affiliation: 

Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-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: 55.92 kDa 
• Atom Count: 3,767 
• Modelled Residue Count: 414 
• Deposited Residue Count: 480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tankyrase-2	A, B [auth C]	240	Homo sapiens	Mutation(s): 0  Gene Names: PARP5B, TANK2, TNKL, TNKS2 EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2K2 (Homo sapiens) Explore Q9H2K2  Go to UniProtKB:  Q9H2K2
PHAROS:  Q9H2K2 GTEx:  ENSG00000107854

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XAV	D [auth A], I [auth C]	2-[4-(trifluoromethyl)phenyl]-7,8-dihydro-5H-thiopyrano[4,3-d]pyrimidin-4-ol C14 H11 F3 N2 O S KLGQSVMIPOVQAX-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], J [auth C], K [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A], L [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], H [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
XAV	BindingDB:  3KR8	Ki: min: 100, max: 100 (nM) from 2 assay(s)
		Kd: min: 4.2, max: 100 (nM) from 5 assay(s)
		IC50: min: 1.9, max: 707 (nM) from 23 assay(s)
	PDBBind:  3KR8	Kd: 8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.255 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.75	α = 90
b = 97.975	β = 90
c = 119.464	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
MOLREP	phasing
REFMAC	refinement
SAINT	data reduction
SAINT	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-15 
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., 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: 2009-12-15
  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