5J47

The X-ray structure of Inhibitor Bound to JCV Helicase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1021/acs.jmedchem.6b00486
  • Primary Citation of Related Structures:  
    5J47, 5J40, 5J4Y, 5J4V

  • 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Large T antigen A372JC polyomavirusMutation(s): 13 
EC: 3.6.4
Find proteins for P03072 (JC polyomavirus)
Explore P03072 
Go to UniProtKB:  P03072
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6JJ
Query on 6JJ

Download Ideal Coordinates CCD File 
A
6-(2-phenoxyphenyl)[1,2,4]triazolo[3,4-b][1,3,4]thiadiazole
C15 H10 N4 O S
KCOSAQLZHSXLNP-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download Ideal Coordinates CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6JJIC50:  4900   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.71α = 90
b = 110.71β = 90
c = 67.75γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2016-03-31 
  • 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