9DNU | pdb_00009dnu

SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun13296

• PDB DOI: https://doi.org/10.2210/pdb9DNU/pdb

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


• Deposited: 2024-09-18 Released: 2025-01-22 
• Deposition Author(s): Ansari, A., Jadhav, P., 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: 2.30 Å
• R-Value Free: 
  0.212 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Design of quinoline SARS-CoV-2 papain-like protease inhibitors as oral antiviral drug candidates.

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

(2025) Nat Commun 16: 1604-1604

• PubMed: 39948104 
• DOI: https://doi.org/10.1038/s41467-025-56902-x
• Primary Citation Related Structures: 
  9DNU, 9DNV, 9DO1, 9DO3, 9DO5, 9DOI


• PubMed Abstract: 
  

  The ever-evolving SARS-CoV-2 variants necessitate the development of additional oral antivirals. This study presents the systematic design of quinoline-containing SARS-CoV-2 papain-like protease (PL ^pro ) inhibitors as potential oral antiviral drug candidates. By leveraging the recently discovered Val70 ^Ub binding site in PL ^pro , we designed a series of quinoline analogs demonstrating potent PL ^pro inhibition and antiviral activity. Notably, the X-ray crystal structures of 6 lead compounds reveal that the 2-aryl substitution can occupy either the Val70 ^Ub site as expected or the BL2 groove in a flipped orientation. The in vivo lead Jun13296 exhibits favorable pharmacokinetic properties and potent inhibition against SARS-CoV-2 variants and nirmatrelvir-resistant mutants. In a mouse model of SARS-CoV-2 infection, oral treatment with Jun13296 significantly improves survival, reduces body weight loss and lung viral titers, and prevents lung tissue damage. These results underscore the potential of quinoline PL ^pro inhibitors as promising oral SARS-CoV-2 antiviral candidates, instilling hope for the future of SARS-CoV-2 treatment.

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.22 kDa 
• Atom Count: 2,776 
• Modeled Residue Count: 311 
• 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  Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BEG (Subject of Investigation/LOI)	B [auth A]	2-methyl-5-[(1R,5S)-8-methyl-3,8-diazabicyclo[3.2.1]octan-3-yl]-N-{(1R)-1-[(2P)-2-(1-methyl-1H-pyrazol-4-yl)quinolin-4-yl]ethyl}benzamide C30 H34 N6 O WOYUEECHXFGKHF-UHFFFAOYSA-N
ZN	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	P [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	L [auth A], M [auth A], N [auth A], O [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.212 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.666	α = 90
b = 113.666	β = 90
c = 220.001	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Ansari, A., Jadhav, P., 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: 2025-01-22
  Type: Initial release
  
• Version 1.1: 2025-02-26
  Changes: Database references