4K4F

Co-crystal structure of TNKS1 with compound 18 [4-[(4S)-5,5-dimethyl-2-oxo-4-phenyl-1,3-oxazolidin-3-yl]-N-(quinolin-8-yl)benzamide]

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.280 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Discovery of novel, induced-pocket binding oxazolidinones as potent, selective, and orally bioavailable tankyrase inhibitors.

Bregman, H., Chakka, N., Guzman-Perez, A., Gunaydin, H., Gu, Y., Huang, X., Berry, V., Liu, J., Teffera, Y., Huang, L., Egge, B., Mullady, E.L., Schneider, S., Andrews, P.S., Mishra, A., Newcomb, J., Serafino, R., Strathdee, C.A., Turci, S.M., Wilson, C., Dimauro, E.F.

(2013) J Med Chem 56: 4320-4342

  • DOI: 10.1021/jm4000038
  • Primary Citation of Related Structures:  
    4K4E, 4K4F

  • PubMed Abstract: 

    • Tankyrase (TNKS) is a poly-ADP-ribosylating protein (PARP) whose activity suppresses cellular axin protein levels and elevates β-catenin concentrations, resulting in increased oncogene expression. The inhibition of tankyrase (TNKS1 and 2) may reduce the ...

    Tankyrase (TNKS) is a poly-ADP-ribosylating protein (PARP) whose activity suppresses cellular axin protein levels and elevates β-catenin concentrations, resulting in increased oncogene expression. The inhibition of tankyrase (TNKS1 and 2) may reduce the levels of β-catenin-mediated transcription and inhibit tumorigenesis. Compound 1 is a previously described moderately potent tankyrase inhibitor that suffers from poor pharmacokinetic properties. Herein, we describe the utilization of structure-based design and molecular modeling toward novel, potent, and selective tankyrase inhibitors with improved pharmacokinetic properties (39, 40).

    Organizational Affiliation: 

    Department of Chemistry Research and Discovery, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, USA. hbregman@amgen.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tankyrase-1 A, B217Homo sapiensMutation(s): 0 
Gene Names: TNKS, PARP5A, PARPL, TIN1, TINF1, TNKS1
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
GTEx:  ENSG00000173273
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K4F
Query on K4F
Download Ideal Coordinates CCD File 
A, B
4-[(4S)-5,5-dimethyl-2-oxo-4-phenyl-1,3-oxazolidin-3-yl]-N-(quinolin-8-yl)benzamide
C27 H23 N3 O3
LUYWAGVRXKSNLL-DEOSSOPVSA-N		 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 %)
K4FIC50 :  200   nM  PDBBind
K4FIC50:  189   nM  BindingDB
K4FIC50:  198   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.280 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.687α = 90
b = 78.121β = 90
c = 146.644γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references