8UUV | pdb_00008uuv

SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun12197

• PDB DOI: https://doi.org/10.2210/pdb8UUV/pdb

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


• Deposited: 2023-11-02 Released: 2024-04-03 
• Deposition Author(s): Ansari, A., Tan, B., Arnold, E., Ruiz, F.X., Wang, J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 
  0.224 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Design of a SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model.

Tan, B., Zhang, X., Ansari, A., Jadhav, P., Tan, H., Li, K., Chopra, A., Ford, A., Chi, X., Ruiz, F.X., Arnold, E., Deng, X., Wang, J.

(2024) Science 383: 1434-1440

• PubMed: 38547259 
• DOI: https://doi.org/10.1126/science.adm9724
• Primary Citation Related Structures: 
  8UOB, 8UUF, 8UUG, 8UUH, 8UUU, 8UUV, 8UUW, 8UUY, 8UVM


• PubMed Abstract: 
  

  The emergence of SARS-CoV-2 variants and drug-resistant mutants calls for additional oral antivirals. The SARS-CoV-2 papain-like protease (PL ^pro ) is a promising but challenging drug target. We designed and synthesized 85 noncovalent PL ^pro inhibitors that bind to a recently discovered ubiquitin binding site and the known BL2 groove pocket near the S4 subsite. Leads inhibited PL ^pro with the inhibitory constant K _i values from 13.2 to 88.2 nanomolar. The co-crystal structures of PL ^pro with eight leads revealed their interaction modes. The in vivo lead Jun12682 inhibited SARS-CoV-2 and its variants, including nirmatrelvir-resistant strains with EC ₅₀ from 0.44 to 2.02 micromolar. Oral treatment with Jun12682 improved survival and reduced lung viral loads and lesions in a SARS-CoV-2 infection mouse model, suggesting that PL ^pro inhibitors are promising oral SARS-CoV-2 antiviral candidates.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.
Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA.
Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.
Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.
Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA.
Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK 74078, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 36.96 kDa 
• Atom Count: 2,549 
• Modeled Residue Count: 307 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A	318	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  EC: 3.4.19.12
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y2I (Subject of Investigation/LOI)	B [auth A]	N-{(1R)-1-[(3P,5P)-3-(1-cyclopropyl-1H-pyrazol-4-yl)-5-(1-methyl-1H-pyrazol-4-yl)phenyl]ethyl}-5-[2-(dimethylamino)ethoxy]-2-methylbenzamide C30 H36 N6 O2 IVASDCDNDJPYPH-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	I [auth A], J [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free:  0.224 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.212	α = 90
b = 114.212	β = 90
c = 218.533	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-04-03 
Deposition Author(s): Ansari, A., Tan, B., Arnold, E., Ruiz, F.X., Wang, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2024-04-03
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Database references