2.1 A resolution structure of Norovirus 3CL protease in complex with inhibitor 7g

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report

This is version 2.1 of the entry. See complete history


Structure-Guided Optimization of Dipeptidyl Inhibitors of Norovirus 3CL Protease.

Rathnayake, A.D.Kim, Y.Dampalla, C.S.Nguyen, H.N.Jesri, A.M.Kashipathy, M.M.Lushington, G.H.Battaile, K.P.Lovell, S.Chang, K.O.Groutas, W.C.

(2020) J Med Chem 63: 11945-11963

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01252
  • Primary Citation of Related Structures:  
    6W5H, 6W5J, 6W5K, 6W5L

  • PubMed Abstract: 

    Acute gastroenteritis caused by noroviruses has a major impact on public health worldwide in terms of morbidity, mortality, and economic burden. The disease impacts most severely immunocompromised patients, the elderly, and children. The current lack of approved vaccines and small-molecule therapeutics for the treatment and prophylaxis of norovirus infections underscores the need for the development of norovirus-specific drugs. The studies described herein entail the use of the gem -dimethyl moiety as a means of improving the pharmacological activity and physicochemical properties of a dipeptidyl series of transition state inhibitors of norovirus 3CL protease, an enzyme essential for viral replication. Several compounds were found to be potent inhibitors of the enzyme in biochemical and cell-based assays. The pharmacological activity and cellular permeability of the inhibitors were found to be sensitive to the location of the gem -dimethyl group.

  • Organizational Affiliation

    LiS Consulting, Lawrence, Kansas 66046, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
188Norovirus Hu/1968/USMutation(s): 0 
Gene Names: ORF1
EC: (PDB Primary Data), (PDB Primary Data), (PDB Primary Data)
Find proteins for Q83883 (Norwalk virus (strain GI/Human/United States/Norwalk/1968))
Explore Q83883 
Go to UniProtKB:  Q83883
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ83883
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T0D (Subject of Investigation/LOI)
Query on T0D

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]
C26 H38 Cl N3 O9 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.435α = 91.65
b = 37.859β = 96.44
c = 115.535γ = 95.44
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

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 StatesR01 AI109039
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30 GM110761

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 2.0: 2020-11-04
    Changes: Database references, Non-polymer description
  • Version 2.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description