3UDD

Tankyrase-1 in complex with small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

[1,2,4]triazol-3-ylsulfanylmethyl)-3-phenyl-[1,2,4]oxadiazoles: antagonists of the Wnt pathway that inhibit tankyrases 1 and 2 via novel adenosine pocket binding.

Shultz, M.D.Kirby, C.A.Stams, T.Chin, D.N.Blank, J.Charlat, O.Cheng, H.Cheung, A.Cong, F.Feng, Y.Fortin, P.D.Hood, T.Tyagi, V.Xu, M.Zhang, B.Shao, W.

(2012) J.Med.Chem. 55: 1127-1136

  • DOI: 10.1021/jm2011222

  • PubMed Abstract: 
  • The Wnt signaling pathway is critical to the regulation of key cellular processes. When deregulated, it has been shown to play a crucial role in the growth and progression of multiple human cancers. The identification of small molecule modulators of ...

    The Wnt signaling pathway is critical to the regulation of key cellular processes. When deregulated, it has been shown to play a crucial role in the growth and progression of multiple human cancers. The identification of small molecule modulators of Wnt signaling has proven challenging, largely due to the relative paucity of druggable nodes in this pathway. Several recent publications have identified small molecule inhibitors of the Wnt pathway, and tankyrase (TNKS) inhibition has been demonstrated to antagonize Wnt signaling via axin stabilization. Herein, we report the early hit assessment of a series of compounds previously reported to antagonize Wnt signaling. We report the biophysical, computational characterization, structure-activity relationship, and physicochemical properties of a novel series of [1,2,4]triazol-3-ylsulfanylmethyl)-3-phenyl-[1,2,4]oxadiazole inhibitors of TNKS1 and 2. Furthermore, a cocrystal structure of compound 24 complexed to TNKS1 demonstrates an alternate binding mode for PARP family member proteins that does not involve interactions with the nicotinamide binding pocket.


    Organizational Affiliation

    Novartis Institutes for Biomedical Research, Inc., Cambridge, Massachusetts 02319, United States. michael.shultz@novartis.com




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
34M
Query on 34M

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A, B
3-(4-methoxyphenyl)-5-({[4-(4-methoxyphenyl)-5-methyl-4H-1,2,4-triazol-3-yl]sulfanyl}methyl)-1,2,4-oxadiazole
C20 H19 N5 O3 S
LQZSHPITKSPDLC-UHFFFAOYSA-N
 Ligand Interaction
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
34MKd: 28 - 79 nM (88) BINDINGDB
34MIC50: 33 nM (88) BINDINGDB
34MKd: 79 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 124.320α = 90.00
b = 44.690β = 90.17
c = 88.200γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTERphasing
BUSTERrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-10-28 
  • Released Date: 2012-02-01 
  • Deposition Author(s): Kirby, C.A., Stams, T.

Revision History 

  • Version 1.0: 2012-02-01
    Type: Initial release
  • Version 1.1: 2012-04-18
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description