4K4F | pdb_00004k4f

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 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.280 (Depositor), 0.273 (DCC) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/jm4000038
  • Primary Citation 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 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

Macromolecule Content 

  • Total Structure Weight: 51.09 kDa 
  • Atom Count: 3,360 
  • Modeled Residue Count: 413 
  • Deposited Residue Count: 434 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tankyrase-1
A, B
217Homo sapiensMutation(s): 0 
Gene Names: TNKSPARP5APARPLTIN1TINF1TNKS1
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O95271 (Homo sapiens)
Explore O95271 
Go to UniProtKB:  O95271
PHAROS:  O95271
GTEx:  ENSG00000173273 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95271
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.290 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.280 (Depositor), 0.273 (DCC) 
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

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations