8UIF

Crystal structure of SARS CoV-2 3CL protease in complex with GSK4365096A

• PDB DOI: https://doi.org/10.2210/pdb8UIF/pdb

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


• Deposited: 2023-10-10 Released: 2024-02-14 
• Deposition Author(s): Concha, N.O., Williams, S.P.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.220 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

Exploration of the P1 residue in 3CL protease inhibitors leading to the discovery of a 2-tetrahydrofuran P1 replacement.

Barton, L.S., Callahan, J.F., Cantizani, J., Concha, N.O., Cotillo Torrejon, I., Goodwin, N.C., Joshi-Pangu, A., Kiesow, T.J., McAtee, J.J., Mellinger, M., Nixon, C.J., Padron-Barthe, L., Patterson, J.R., Pearson, N.D., Pouliot, J.J., Rendina, A.R., Buitrago Santanilla, A., Schneck, J.L., Sanz, O., Thalji, R.K., Ward, P., Williams, S.P., King, B.W.

(2024) Bioorg Med Chem 100: 117618-117618

• PubMed: 38309201 
• DOI: https://doi.org/10.1016/j.bmc.2024.117618
• Primary Citation of Related Structures:  
  8UHO, 8UIA, 8UIF, 8ULD


• PubMed Abstract: 
  

  The virally encoded 3C-like protease (3CL ^pro ) is a well-validated drug target for the inhibition of coronaviruses including Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Most inhibitors of 3CL ^pro are peptidomimetic, with a γ-lactam in place of Gln at the P1 position of the pseudopeptide chain. An effort was pursued to identify a viable alternative to the γ-lactam P1 mimetic which would improve physicochemical properties while retaining affinity for the target. Discovery of a 2-tetrahydrofuran as a suitable P1 replacement that is a potent enzymatic inhibitor of 3CL ^pro in SARS-CoV-2 virus is described herein.

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Organizational Affiliation: 

GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States. Electronic address: [e-mail].

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)

Macromolecule Content

• Total Structure Weight: 68.9 kDa 
• Atom Count: 4,881 
• Modelled Residue Count: 606 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	306	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
A1ADS (Subject of Investigation/LOI)	C [auth A], D [auth B]	N-[(benzyloxy)carbonyl]-4-fluoro-L-phenylalanyl-N-{(2R)-1-[(2S)-oxolan-2-yl]-3-[(3S)-2-oxooxolan-3-yl]propan-2-yl}-L-leucinamide C34 H44 F N3 O7 KTLVPXDSLURVFT-WJBPYKOESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.220 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.724	α = 90
b = 100.404	β = 90
c = 103.116	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-14 
Deposition Author(s): Concha, N.O., Williams, S.P.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2024-02-14
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Structure summary