5WEJ | pdb_00005wej

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

• PDB DOI: https://doi.org/10.2210/pdb5WEJ/pdb

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


• Deposited: 2017-07-10 Released: 2017-12-13 
• Deposition Author(s): Lovell, S., Battaile, K.P., Mehzabeen, N., Damalanka, V.C., Kim, Y., Kankanamalage, A.C.G., Rathnayake, A.D., Nguyen, H.N., Chang, K.O., Groutas, W.C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.229 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Structure-guided design, synthesis and evaluation of oxazolidinone-based inhibitors of norovirus 3CL protease.

Damalanka, V.C., Kim, Y., Galasiti Kankanamalage, A.C., Rathnayake, A.D., Mehzabeen, N., Battaile, K.P., Lovell, S., Nguyen, H.N., Lushington, G.H., Chang, K.O., Groutas, W.C.

(2017) Eur J Med Chem 143: 881-890

• PubMed: 29227928 
• DOI: https://doi.org/10.1016/j.ejmech.2017.12.014
• Primary Citation Related Structures: 
  5WEJ


• PubMed Abstract: 
  

  Acute nonbacterial gastroenteritis caused by noroviruses constitutes a global public health concern and a significant economic burden. There are currently no small molecule therapeutics or vaccines for the treatment of norovirus infections. A structure-guided approach was utilized in the design of a series of inhibitors of norovirus 3CL protease that embody an oxazolidinone ring as a novel design element for attaining optimal binding interactions. Low micromolar cell-permeable inhibitors that display anti-norovirus activity have been identified. The mechanism of action, mode of binding, and structural rearrangements associated with the interaction of the inhibitors and the enzyme were elucidated using X-ray crystallography.

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Organizational Affiliation: 
• Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.
Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA.
IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, IL 60439, USA.
LiS Consulting, Lawrence, KS 66046, USA.
Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA. Electronic address: [e-mail].
Department of Chemistry, Wichita State University, Wichita, KS 67260, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.18 kDa 
• Atom Count: 2,625 
• Modeled Residue Count: 334 
• Deposited Residue Count: 376 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V45	C [auth A], D [auth B]	(2S)-2-{(5S)-5-[(3-chlorophenyl)methyl]-2-oxo-1,3-oxazolidin-3-yl}-4-methyl-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}pentanamide C23 H30 Cl N3 O5 HPMLVVHQNDVVJA-ZXBFEJPJSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.229 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.556	α = 90
b = 59.556	β = 90
c = 357.548	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-12-13 
Deposition Author(s): Lovell, S., Battaile, K.P., Mehzabeen, N., Damalanka, V.C., Kim, Y., Kankanamalage, A.C.G., Rathnayake, A.D., Nguyen, H.N., Chang, K.O., Groutas, W.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI109039
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM110761

Revision History  

• Version 1.0: 2017-12-13
  Type: Initial release
  
• Version 1.1: 2017-12-27
  Changes: Database references
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary