5J4V

The crystal structure of Inhibitor Bound to JCV Helicase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.169 

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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6JH
Query on 6JH
Download Ideal Coordinates CCD File 
A
2-(2-phenoxypyridin-3-yl)[1,3]thiazolo[5,4-c]pyridine
C17 H11 N3 O S
BEFVRNYCLDLVCZ-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
SO4
Query on SO4
Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.169 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.92α = 90
b = 109.92β = 90
c = 66.86γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2016-04-01 
  • 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