4LI8

TANKYRASE-1 complexed with small molecule inhibitor 2-[4-(4-fluorobenzoyl)piperidin-1-yl]-N-[(4-oxo-3,5,7,8-tetrahydro-4H-pyrano[4,3-d]pyrimidin-2-yl)methyl]-N-(thiophen-2-ylmethyl)acetamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1XQ
Query on 1XQ

Download Ideal Coordinates CCD File 
A, B
2-[4-(4-fluorobenzoyl)piperidin-1-yl]-N-[(4-oxo-3,5,7,8-tetrahydro-4H-pyrano[4,3-d]pyrimidin-2-yl)methyl]-N-(thiophen-2-ylmethyl)acetamide
C27 H29 F N4 O4 S
SUKHPNUTRMBUST-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1XQIC50 :  7.5   nM  PDBBind
1XQIC50:  7.5   nM  BindingDB
1XQIC50:  15.399999618530273   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.7α = 90
b = 43.1β = 91.3
c = 88.1γ = 90
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata 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