7JRN

Crystal structure of the wild type SARS-CoV-2 papain-like protease (PLPro) with inhibitor GRL0617

• PDB DOI:  https://doi.org/10.2210/pdb7JRN/pdb

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


• Deposited: 2020-08-12 Released: 2020-08-26 
• Deposition Author(s): Sacco, M., Ma, C., Wang, J., Chen, Y.
• 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: 2.48 Å
• R-Value Free: 0.287 
• R-Value Work: 0.245 
• R-Value Observed: 0.247 

Literature

Discovery of SARS-CoV-2 Papain-like Protease Inhibitors through a Combination of High-Throughput Screening and a FlipGFP-Based Reporter Assay.

Ma, C., Sacco, M.D., Xia, Z., Lambrinidis, G., Townsend, J.A., Hu, Y., Meng, X., Szeto, T., Ba, M., Zhang, X., Gongora, M., Zhang, F., Marty, M.T., Xiang, Y., Kolocouris, A., Chen, Y., Wang, J.

(2021) ACS Cent Sci 7: 1245-1260

• PubMed: 34341772 
• DOI: https://doi.org/10.1021/acscentsci.1c00519
• Primary Citation of Related Structures:  
  7JRN


• PubMed Abstract: 
  

The papain-like protease (PL ^pro ) of SARS-CoV-2 is a validated antiviral drug target. Through a fluorescence resonance energy transfer-based high-throughput screening and subsequent lead optimization, we identified several PL ^pro inhibitors including Jun9-72-2 and Jun9-75-4 with improved enzymatic inhibition and antiviral activity compared to GRL0617 , which was reported as a SARS-CoV PL ^pro inhibitor. Significantly, we developed a cell-based FlipGFP assay that can be applied to predict the cellular antiviral activity of PL ^pro inhibitors in the BSL-2 setting. X-ray crystal structure of PL ^pro in complex with GRL0617 showed that binding of GRL0617 to SARS-CoV-2 induced a conformational change in the BL2 loop to a more closed conformation. Molecular dynamics simulations showed that Jun9-72-2 and Jun9-75-4 engaged in more extensive interactions than GRL0617 . Overall, the PL ^pro inhibitors identified in this study represent promising candidates for further development as SARS-CoV-2 antivirals, and the FlipGFP-PL ^pro assay is a suitable surrogate for screening PL ^pro inhibitors in the BSL-2 setting.

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Organizational Affiliation: 

Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 74.71 kDa 
• Atom Count: 5,160 
• Modelled Residue Count: 630 
• Deposited Residue Count: 646 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A, B [auth J]	323	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 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
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
TTT (Subject of Investigation/LOI)	C [auth A], G [auth J]	5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide C20 H20 N2 O UVERBUNNCOKGNZ-CQSZACIVSA-N
SO4	E [auth A], F [auth A], I [auth J], J, K [auth J]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	D [auth A], H [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.287 
• R-Value Work: 0.245 
• R-Value Observed: 0.247 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.733	α = 90
b = 144.872	β = 99.26
c = 60.145	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
HKL-3000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-26 
Deposition Author(s): Sacco, M., Ma, C., Wang, J., Chen, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI147325

Revision History  

• Version 1.0: 2020-08-26
  Type: Initial release
  
• Version 1.1: 2021-01-27
  Changes: Structure summary
• Version 1.2: 2021-09-08
  Changes: Database references