3UH4

TANKYRASE-1 complexed with NVP-XAV939


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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 68: 115-118

  • DOI: 10.1107/S1744309111051219
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tankyrase-1
A, B
224Homo sapiensMutation(s): 0 
Gene Names: TNKS (PARP5A, PARPL, TIN1, TINF1, TNKS1)
EC: 2.4.2.30
Find proteins for O95271 (Homo sapiens)
Go to Gene View: TNKS
Go to UniProtKB:  O95271
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
XAV
Query on XAV

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A, 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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XAVIC50: 4 - 68 nM (88) BINDINGDB
XAVKd: 8 - 100 nM (99) BINDINGDB
XAVIC50: 11 nM BINDINGMOAD
XAVIC50: 11 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 123.915α = 90.00
b = 45.239β = 90.44
c = 88.135γ = 90.00
Software Package:
Software NamePurpose
BUSTERphasing
XDSdata reduction
BUSTERrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-11-03 
  • 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
    Type: Refinement description