4K4E

Co-crystal structure of tnks1 with compound 52 [N~2-(5-chloro-2-methoxyphenyl)-N-[trans-4-(2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)cyclohexyl]glycinamide]


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.250 

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 AB217Homo sapiensMutation(s): 0 
Gene Names: TNKSPARP5APARPLTIN1TINF1TNKS1
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K4E
Query on K4E

Download Ideal Coordinates CCD File 
A, B
N~2~-(5-chloro-2-methoxyphenyl)-N-[trans-4-(2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)cyclohexyl]glycinamide
C22 H25 Cl N4 O3
ACLPRRFIFVCSJV-WKILWMFISA-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 %)
K4EIC50 :  24   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.250 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.44α = 90
b = 73.264β = 90
c = 149.059γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-04-12 
  • Released Date: 2013-06-05 
  • Deposition Author(s): Huang, X.

Revision History 

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