6BIB

1.95 A resolution structure of Norovirus 3CL protease in complex with a triazole-based macrocyclic inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Putative structural rearrangements associated with the interaction of macrocyclic inhibitors with norovirus 3CL protease.

Galasiti Kankanamalage, A.C.Weerawarna, P.M.Rathnayake, A.D.Kim, Y.Mehzabeen, N.Battaile, K.P.Lovell, S.Chang, K.O.Groutas, W.C.

(2019) Proteins 87: 579-587

  • DOI: 10.1002/prot.25682
  • Primary Citation of Related Structures:  
    6BIB, 6BID, 6BIC

  • PubMed Abstract: 
  • Human noroviruses are the primary cause of outbreaks of acute gastroenteritis worldwide. The problem is further compounded by the current lack of norovirus-specific antivirals or vaccines. Noroviruses have a single-stranded, positive sense 7 to 8 kb RNA genome which encodes a polyprotein precursor that is processed by a virus-encoded 3C-like cysteine protease (NV 3CLpro) to generate at least six mature nonstructural proteins ...

    Human noroviruses are the primary cause of outbreaks of acute gastroenteritis worldwide. The problem is further compounded by the current lack of norovirus-specific antivirals or vaccines. Noroviruses have a single-stranded, positive sense 7 to 8 kb RNA genome which encodes a polyprotein precursor that is processed by a virus-encoded 3C-like cysteine protease (NV 3CLpro) to generate at least six mature nonstructural proteins. Processing of the polyprotein is essential for virus replication, consequently, NV 3CLpro has emerged as an attractive target for the discovery of norovirus therapeutics and prophylactics. We have recently described the structure-based design of macrocyclic transition state inhibitors of NV 3CLpro. In order to gain insight and understanding into the interaction of macrocyclic inhibitors with the enzyme, as well as probe the effect of ring size on pharmacological activity and cellular permeability, additional macrocyclic inhibitors were synthesized and high resolution cocrystal structures determined. The results of our studies tentatively suggest that the macrocyclic scaffold may hamper optimal binding to the active site by impeding concerted cross-talk between the S 2 and S 4 subsites.


    Organizational Affiliation

    Department of Chemistry, Wichita State University, Kansas.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteaseA, B188Norovirus Hu/1968/USMutation(s): 0 
Gene Names: ORF1
EC: 3.4.22.66 (PDB Primary Data), 3.6.1.15 (UniProt), 2.7.7.48 (UniProt)
Find proteins for Q83883 (Norwalk virus (strain GI/Human/United States/Norwalk/1968))
Explore Q83883 
Go to UniProtKB:  Q83883
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DW7
Query on DW7

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]benzyl [(9S,12S,15S)-12-(cyclohexylmethyl)-9-(hydroxymethyl)-6,11,14-trioxo-1,5,10,13,18,19-hexaazabicyclo[15.2.1]icosa-17(20),18-dien-15-yl]carbamate
C30 H43 N7 O6
DATPOADEZAYIPB-RNXOBYDBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.873α = 90
b = 67.191β = 90
c = 126.576γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI109039
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30GM110761

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.3: 2019-06-12
    Changes: Data collection, Database references
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence