Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.83 kDa 
• Atom Count: 1,403 
• Modelled Residue Count: 165 
• Deposited Residue Count: 188 
• Unique protein chains: 1

 4XBB

1.85A resolution structure of Norovirus 3CL protease complex with a covalently bound dipeptidyl inhibitor diethyl [(1R,2S)-2-[(N-{[(3-chlorobenzyl)oxy]carbonyl}-3-cyclohexyl-L-alanyl)amino]-1-hydroxy-3-(2-oxo-2H-pyrrol-3-yl)propyl]phosphonate

• PDB DOI:  https://doi.org/10.2210/pdb4XBB/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Norovirus Hu/1968/US
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-12-16 Released: 2015-03-25 
• Deposition Author(s): Lovell, S., Battaile, K.P., Mehzabeen, N., Kankanamalage, A.C.G., Kim, Y., Weerawarna, P.M., Uy, R.A.Z., Damalanka, V.C., Mandadapu, S.R., Alliston, K.R., Groutas, W.C., Chang, K.-O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.197 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 

Literature

Structure-Guided Design and Optimization of Dipeptidyl Inhibitors of Norovirus 3CL Protease. Structure-Activity Relationships and Biochemical, X-ray Crystallographic, Cell-Based, and In Vivo Studies.

Galasiti Kankanamalage, A.C., Kim, Y., Weerawarna, P.M., Uy, R.A., Damalanka, V.C., Mandadapu, S.R., Alliston, K.R., Mehzabeen, N., Battaile, K.P., Lovell, S., Chang, K.O., Groutas, W.C.

(2015) J Med Chem 58: 3144-3155

• PubMed: 25761614 
• DOI: https://doi.org/10.1021/jm5019934
• Primary Citation of Related Structures:  
  4XBB, 4XBC, 4XBD


• PubMed Abstract: 
  

Norovirus infection constitutes the primary cause of acute viral gastroenteritis. There are currently no vaccines or norovirus-specific antiviral therapeutics available for the management of norovirus infection. Norovirus 3C-like protease is essential for viral replication, consequently, inhibition of this enzyme is a fruitful avenue of investigation that may lead to the emergence of antinorovirus therapeutics. We describe herein the optimization of dipeptidyl inhibitors of norovirus 3C-like protease using iterative SAR, X-ray crystallographic, and enzyme and cell-based studies. We also demonstrate herein in vivo efficacy of an inhibitor using the murine model of norovirus infection.

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Organizational Affiliation: 

†Department of Chemistry, Wichita State University, 1845 North Fairmount Avenue, Wichita, Kansas 67260, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-LIKE PROTEASE	A	188	Norovirus Hu/1968/US	Mutation(s): 0  Gene Names: ORF1 EC: 3.4.22.66 (PDB Primary Data), 3.6.1.15 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q83883 (Norwalk virus (strain GI/Human/United States/Norwalk/1968)) Explore Q83883  Go to UniProtKB:  Q83883

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3ZR	B [auth A]	diethyl [(1R,2S)-2-[(N-{[(3-chlorobenzyl)oxy]carbonyl}-3-cyclohexyl-L-alanyl)amino]-1-hydroxy-3-(2-oxo-2H-pyrrol-3-yl)propyl]phosphonate C28 H39 Cl N3 O8 P MWLFTRMZFWFMSR-HFKGTQBBSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.197 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.171	α = 90
b = 124.171	β = 90
c = 49.969	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-25 
Deposition Author(s): Lovell, S., Battaile, K.P., Mehzabeen, N., Kankanamalage, A.C.G., Kim, Y., Weerawarna, P.M., Uy, R.A.Z., Damalanka, V.C., Mandadapu, S.R., Alliston, K.R., Groutas, W.C., Chang, K.-O.

Revision History  

• Version 1.0: 2015-03-25
  Type: Initial release
  
• Version 1.1: 2015-04-22
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Advisory, Database references, Derived calculations, Refinement description, Source and taxonomy
• Version 1.3: 2018-01-17
  Changes: Author supporting evidence