3UH4

TANKYRASE-1 complexed with NVP-XAV939

• PDB DOI: https://doi.org/10.2210/pdb3UH4/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-11-03 Released: 2012-02-15 
• Deposition Author(s): Stams, T., Kirby, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.234 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 

Literature

Structure of human tankyrase 1 in complex with small-molecule inhibitors PJ34 and XAV939.

Kirby, C.A., Cheung, A., Fazal, A., Shultz, M.D., Stams, T.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 115-118

• PubMed: 22297980 
• DOI: https://doi.org/10.1107/S1744309111051219
• Primary Citation of Related Structures:  
  3UH2, 3UH4


• PubMed Abstract: 
  

  The crystal structures of tankyrase 1 (TNKS1) in complex with two small-molecule inhibitors, PJ34 and XAV939, both at 2.0 Å resolution, are reported. The structure of TNKS1 in complex with PJ34 reveals two molecules of PJ34 bound in the NAD(+) donor pocket. One molecule is in the nicotinamide portion of the pocket, as previously observed in other PARP structures, while the second molecule is bound in the adenosine portion of the pocket. Additionally, unlike the unliganded crystallization system, the TNKS1-PJ34 crystallization system has the NAD(+) donor site accessible to bulk solvent in the crystal, which allows displacement soaking. The TNKS1-PJ34 crystallization system was used to determine the structure of TNKS1 in complex with XAV939. These structures provide a basis for the start of a structure-based drug-design campaign for TNKS1.

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Organizational Affiliation: 

Novartis Institute for Biomedical Research, Cambridge, MA 02139, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.52 kDa 
• Atom Count: 3,787 
• Modelled Residue Count: 420 
• Deposited Residue Count: 448 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tankyrase-1	A, B	224	Homo sapiens	Mutation(s): 1  EC: 2.4.2.30
UniProt & NIH Common Fund Data Resources
Find proteins for O95271 (Homo sapiens) Explore O95271  Go to UniProtKB:  O95271
PHAROS:  O95271 GTEx:  ENSG00000173273

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XAV	D [auth A], K [auth B]	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], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth A], O [auth B], P [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
XAV	BindingDB:  3UH4	Kd: min: 4.2, max: 100 (nM) from 5 assay(s)
		IC50: min: 2.1, max: 95 (nM) from 18 assay(s)
	Binding MOAD:  3UH4	IC50: 11 (nM) from 1 assay(s)
	PDBBind:  3UH4	IC50: 11 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.234 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.915	α = 90
b = 45.239	β = 90.44
c = 88.135	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-15 
Deposition Author(s): Stams, T., Kirby, C.

Revision History  

• Version 1.0: 2012-02-15
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations