1.85 A resolution structure of Norovirus 3CL protease in complex with inhibitor 7d

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

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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
187Norovirus Hu/1968/USMutation(s): 0 
Gene Names: ORF1
Find proteins for Q83883 (Norovirus (strain Human/NoV/United States/Norwalk/1968/GI))
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
TKS (Subject of Investigation/LOI)
Query on TKS

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2-(3-chlorophenyl)-2-methylpropyl [(2S)-3-cyclohexyl-1-({(1R,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-1-sulfanylpropan-2-yl}amino)-1-oxopropan-2-yl]carbamate
C27 H40 Cl N3 O5 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.469α = 90
b = 34.986β = 97.6
c = 111.473γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

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 1.1: 2020-11-04
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description