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: 2.3 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:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tankyrase-1
A, B
217Homo sapiensMutation(s): 0 
Gene Names: TNKS (PARP5A, PARPL, TIN1, TINF1, TNKS1)
EC: 2.4.2.30
Find proteins for O95271 (Homo sapiens)
Go to Gene View: TNKS
Go to UniProtKB:  O95271
Small Molecules
Ligands 2 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
K4E
Query on K4E

Download SDF File 
Download 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
K4EIC50: 24 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.250 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.440α = 90.00
b = 73.264β = 90.00
c = 149.059γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
AMoREphasing
HKL-2000data scaling
CNSrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references