4N4T

Co-crystal structure of tankyrase 1 with compound 3 [(4S)-3-{4-[6-amino-5-(pyrimidin-2-yl)pyridin-3-yl]phenyl}-5,5-dimethyl-4-phenyl-1,3-oxazolidin-2-one]


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.251 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure-based design of 2-aminopyridine oxazolidinones as potent and selective tankyrase inhibitors.

Huang, H.Guzman-Perez, A.Acquaviva, L.Berry, V.Bregman, H.Dovey, J.Gunaydin, H.Huang, X.Huang, L.Saffran, D.Serafino, R.Schneider, S.Wilson, C.DiMauro, E.F.

(2013) ACS Med Chem Lett 4: 1218-1223

  • DOI: https://doi.org/10.1021/ml4003315
  • Primary Citation of Related Structures:  
    4N3R, 4N4T, 4N4V

  • PubMed Abstract: 

    Aberrant activation of the Wnt pathway has been implicated in the development and formation of many cancers. TNKS inhibition has been shown to antagonize Wnt signaling via Axin stabilization in APC mutant colon cancer cell lines. We employed structure-based design to identify a series of 2-aminopyridine oxazolidinones as potent and selective TNKS inhibitors. These compounds exhibited good enzyme and cell potency as well as selectivity over other PARP isoforms. Co-crystal structures of these 2-aminopyridine oxazolidinones complexed to TNKS reveal an induced-pocket binding mode that does not involve interactions with the nicotinamide binding pocket. Oral dosing of lead compounds 3 and 4 resulted in significant effects on several Wnt-pathway biomarkers in a three day DLD-1 mouse tumor PD model.


  • Organizational Affiliation

    Departments of Medicinal Chemistry; Pharmacokinetics and Drug Metabolism; Oncology Research; and Molecular Structure, Amgen Inc. , 360 Binney Street, Cambridge, Massachusetts 02142, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tankyrase-1
A, B
217Mus musculusMutation(s): 0 
Gene Names: TnksTnks1
EC: 2.4.2.30
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PFX9 (Mus musculus)
Explore Q6PFX9 
Go to UniProtKB:  Q6PFX9
IMPC:  MGI:1341087
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PFX9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
2GV Binding MOAD:  4N4T IC50: 49 (nM) from 1 assay(s)
BindingDB:  4N4T IC50: min: 25.9, max: 49 (nM) from 2 assay(s)
PDBBind:  4N4T IC50: 49 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.251 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.944α = 90
b = 77.879β = 90
c = 147.647γ = 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

  • Released Date: 2013-12-11 
  • Deposition Author(s): Huang, X.

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2014-07-02
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations