8F46

Crystal structure of SARS-CoV-2 3CL protease in complex with a dimethyl phenyl sulfane inhibitor (cyano warhead)

• PDB DOI: https://doi.org/10.2210/pdb8F46/pdb

• Classification: HYDROLASE/Inhibitor
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-11-10 Released: 2022-11-23 
• Deposition Author(s): Liu, L., Lovell, S., Cooper, A., Battaile, K.P., Dampalla, C.S., 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: 1.50 Å
• R-Value Free: 0.221 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

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: 69.29 kDa 
• Atom Count: 5,068 
• Modelled Residue Count: 601 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XCK (Subject of Investigation/LOI)	C [auth A], D [auth B]	N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-N~2~-{[2-methyl-2-(phenylsulfanyl)propoxy]carbonyl}-L-leucinamide C24 H36 N4 O4 S ZIDTZUSIKUZLIR-WNPRXXRGSA-N
PG4	E [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.221 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.989	α = 90
b = 98.24	β = 107.8
c = 58.625	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-23 
Deposition Author(s): Liu, L., Lovell, S., Cooper, A., Battaile, K.P., Dampalla, C.S., 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: 2022-11-23
  Type: Initial release
  
• Version 1.1: 2023-04-26
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description