8E65

Crystal structure of SARS-CoV-2 3CL protease in complex with a p-chlorodimethyl oxybenzene inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8E65/pdb

• Classification: HYDROLASE, Viral protein/Inhibitor
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-08-22 Released: 2022-09-14 
• Deposition Author(s): Lovell, S., Liu, L., Battaile, K.P., Miller, M.J., Groutas, W.C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.235 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)

Dampalla, C.S., Miller, M.J., Kim, Y., Zabiegala, A., Nguyen, H.N., Madden, T.K., Thurman, H.A., Machen, A.J., Cooper, A., Liu, L., Battaile, K.P., Lovell, S., Chang, K.O., Groutas, W.C.

(2023) Eur J Med Chem 254: 115376

• DOI: https://doi.org/10.1016/j.ejmech.2023.115376

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 34.65 kDa 
• Atom Count: 2,421 
• Modelled Residue Count: 299 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	309	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WF5	B [auth A]	(1S,2S)-2-[(N-{[2-(4-chlorophenoxy)-2-methylpropoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid C24 H36 Cl N3 O9 S JMICFZXJVQQEHE-BCSOYYNPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.235 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.075	α = 90
b = 53.35	β = 102.34
c = 45.944	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-14 
Deposition Author(s): Lovell, S., Liu, L., Battaile, K.P., Miller, M.J., 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	R01AI161085
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2022-09-14
  Type: Initial release
  
• Version 1.1: 2023-04-26
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description