5J4Y

The crystal structure of N-(4-(2-(thiazolo[5,4-c]pyridin-2-yl)phenoxy)phenyl)acetamide bound to JCV Helicase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Fragment-Based Discovery of Dual JC Virus and BK Virus Helicase Inhibitors.

Bonafoux, D.Nanthakumar, S.Bandarage, U.K.Memmott, C.Lowe, D.Aronov, A.M.Bhisetti, G.R.Bonanno, K.C.Coll, J.Leeman, J.Lepre, C.A.Lu, F.Perola, E.Rijnbrand, R.Taylor, W.P.Wilson, D.Zhou, Y.Zwahlen, J.Ter Haar, E.

(2016) J Med Chem 59: 7138-7151

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b00486
  • Primary Citation of Related Structures:  
    5J40, 5J47, 5J4V, 5J4Y

  • PubMed Abstract: 

    There are currently no treatments for life-threatening infections caused by human polyomaviruses JCV and BKV. We therefore report herein the first crystal structure of the hexameric helicase of JCV large T antigen (apo) and its use to drive the structure-based design of dual JCV and BKV ATP-competitive inhibitors. The crystal structures obtained by soaking our early inhibitors into the JCV helicase allowed us to rapidly improve the biochemical activity of our inhibitors from 18 μM for the early 6-(2-methoxyphenyl)- and the 6-(2-ethoxyphenyl)-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazole hits 1a and 1b to 0.6 μM for triazolopyridine 12i. In addition, we were able to demonstrate measurable antiviral activity in Vero cells for our thiazolopyridine series in the absence of marked cytotoxicity, thus confirming the usefulness of this approach.


  • Organizational Affiliation

    Vertex Pharmaceuticals, Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Large T antigen372JC polyomavirusMutation(s): 13 
EC: 3.6.4 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt
Find proteins for P03072 (JC polyomavirus)
Explore P03072 
Go to UniProtKB:  P03072
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03072
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6JG
Query on 6JG

Download Ideal Coordinates CCD File 
F [auth A]N-{4-[2-([1,3]thiazolo[5,4-c]pyridin-2-yl)phenoxy]phenyl}acetamide
C20 H15 N3 O2 S
OPOGWEXFOKBMCJ-UHFFFAOYSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
C [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.25α = 90
b = 109.25β = 90
c = 66.67γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2016-07-20 
  • Deposition Author(s): Ter Haar, E.

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-08-24
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations