8ULD | pdb_00008uld

SARA CoV-2 3C-like protease in complex with GSK3487016A

• PDB DOI: https://doi.org/10.2210/pdb8ULD/pdb

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


• Deposited: 2023-10-16 Released: 2024-02-14 
• Deposition Author(s): Williams, S.P., Concha, N.O.
• Funding Organization(s): Other private

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

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 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.

---

Organizational Affiliation: 
• GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States. Electronic address: [e-mail].
GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States.
GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain.

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: 36.91 kDa 
• Atom Count: 2,525 
• Modeled Residue Count: 305 
• Deposited Residue Count: 325 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1a	A	325	Severe acute respiratory syndrome coronavirus	Mutation(s): 0  Gene Names: 1a
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus) Explore P0C6X7  Go to UniProtKB:  P0C6X7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WYR (Subject of Investigation/LOI)	B [auth A]	N-[(benzyloxy)carbonyl]-4-fluoro-L-phenylalanyl-N-{(2S,3R)-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]-4-[(propan-2-yl)amino]butan-2-yl}-L-leucinamide C34 H46 F N5 O7 BQVFQZWCCRSJJV-MZCDCCSRSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.835	α = 90
b = 81.918	β = 104.29
c = 53.786	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
MOLREP	phasing
SCALEPACK	data scaling
REFMAC	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

---

Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2024-02-14
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Structure summary