4LI6

TANKYRASE-1 Complexed with small molecule inhibitor N-[(4-oxo-3,4-dihydroquinazolin-2-yl)methyl]-3-phenyl-N-(thiophen-2-ylmethyl)propanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification of NVP-TNKS656: The Use of Structure-Efficiency Relationships To Generate a Highly Potent, Selective, and Orally Active Tankyrase Inhibitor.

Shultz, M.D.Cheung, A.K.Kirby, C.A.Firestone, B.Fan, J.Chen, C.H.Chen, Z.Chin, D.N.Dipietro, L.Fazal, A.Feng, Y.Fortin, P.D.Gould, T.Lagu, B.Lei, H.Lenoir, F.Majumdar, D.Ochala, E.Palermo, M.G.Pham, L.Pu, M.Smith, T.Stams, T.Tomlinson, R.C.Toure, B.B.Visser, M.Wang, R.M.Waters, N.J.Shao, W.

(2013) J Med Chem 56: 6495-6511

  • DOI: 10.1021/jm400807n
  • Primary Citation of Related Structures:  
    4LI6, 4LI7, 4LI8

  • PubMed Abstract: 
  • Tankyrase 1 and 2 have been shown to be redundant, druggable nodes in the Wnt pathway. As such, there has been intense interest in developing agents suitable for modulating the Wnt pathway in vivo by targeting this enzyme pair. By utilizing a combination ...

    Tankyrase 1 and 2 have been shown to be redundant, druggable nodes in the Wnt pathway. As such, there has been intense interest in developing agents suitable for modulating the Wnt pathway in vivo by targeting this enzyme pair. By utilizing a combination of structure-based design and LipE-based structure efficiency relationships, the core of XAV939 was optimized into a more stable, more efficient, but less potent dihydropyran motif 7. This core was combined with elements of screening hits 2, 19, and 33 and resulted in highly potent, selective tankyrase inhibitors that are novel three pocket binders. NVP-TNKS656 (43) was identified as an orally active antagonist of Wnt pathway activity in the MMTV-Wnt1 mouse xenograft model. With an enthalpy-driven thermodynamic signature of binding, highly favorable physicochemical properties, and high lipophilic efficiency, NVP-TNKS656 is a novel tankyrase inhibitor that is well suited for further in vivo validation studies.


    Organizational Affiliation

    Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States. michael.shultz@novartis.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tankyrase-1 AB224Homo sapiensMutation(s): 0 
Gene Names: TNKSPARP5APARPLTIN1TINF1TNKS1
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
Find proteins for O95271 (Homo sapiens)
Explore O95271 
Go to UniProtKB:  O95271
NIH Common Fund Data Resources
PHAROS:  O95271
Protein Feature View
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  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1XOIC50 :  106   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.082α = 90
b = 44.814β = 90.22
c = 87.846γ = 90
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-07-02 
  • Released Date: 2013-08-14 
  • Deposition Author(s): Kirby, C.A., Stams, T.

Revision History 

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-10-02
    Changes: Database references