4J3M

Tankyrase 2 in complex with 3-chloro-4-(4-methyl-2-oxo-1,2-dihydroquinolin-7-yl)benzoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Fragment-based ligand design of novel potent inhibitors of tankyrases.

Larsson, E.A.Jansson, A.E.Ng, F.M.Then, S.W.Panicker, R.Liu, B.Sangthongpitag, K.Pendharkar, V.Tai, S.J.Hill, J.Dan, C.Ho, S.Y.Cheong, W.W.Poulsen, A.Blanchard, S.Lin, G.R.Alam, J.Keller, T.H.Nordlund, P.

(2013) J.Med.Chem. 56: 4497-4508

  • DOI: 10.1021/jm400211f
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tankyrases constitute potential drug targets for cancer and myelin-degrading diseases. We have applied a structure- and biophysics-driven fragment-based ligand design strategy to discover a novel family of potent inhibitors for human tankyrases. Biop ...

    Tankyrases constitute potential drug targets for cancer and myelin-degrading diseases. We have applied a structure- and biophysics-driven fragment-based ligand design strategy to discover a novel family of potent inhibitors for human tankyrases. Biophysical screening based on a thermal shift assay identified highly efficient fragments binding in the nicotinamide-binding site, a local hot spot for fragment binding. Evolution of the fragment hit 4-methyl-1,2-dihydroquinolin-2-one (2) along its 7-vector yields dramatic affinity improvements in the first cycle of expansion. A crystal structure of 7-(2-fluorophenyl)-4-methylquinolin-2(1H)-one (11) reveals that the nonplanar compound extends with its fluorine atom into a pocket, which coincides with a region of the active site where structural differences are seen between tankyrases and other poly(ADP-ribose) polymerase (PARP) family members. A further cycle of optimization yielded compounds with affinities and IC50 values in the low nanomolar range and with good solubility, PARP selectivity, and ligand efficiency.


    Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University, Lab 07-01, 61 Biopolis Drive (Proteos), Singapore 138673. andreas.larsson@ntu.edu.sg




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tankyrase-2
A, B
210Homo sapiensMutation(s): 0 
Gene Names: TNKS2 (PARP5B, TANK2, TNKL)
EC: 2.4.2.30
Find proteins for Q9H2K2 (Homo sapiens)
Go to Gene View: TNKS2
Go to UniProtKB:  Q9H2K2
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
AJ8
Query on AJ8

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Download CCD File 
A, B
3-chloro-4-(4-methyl-2-oxo-1,2-dihydroquinolin-7-yl)benzoic acid
C17 H12 Cl N O3
PGFIIDLKOWRJOX-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AJ8IC50: 21 nM BINDINGMOAD
AJ8IC50: 21 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.171 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 89.531α = 90.00
b = 99.275β = 90.00
c = 114.652γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALAdata scaling
REFMACrefinement
PHASESphasing
HKL-2000data collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-26
    Type: Initial release