7JIW | pdb_00007jiw

The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder530 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb7JIW/pdb

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


• Deposited: 2020-07-23 Released: 2020-08-05 
• Deposition Author(s): Osipiuk, J., Tesar, C., Endres, M., Lisnyak, V., Maki, S., Taylor, C., Zhang, Y., Zhou, Z., Azizi, S.A., Jones, K., Kathayat, R., Snyder, S.A., Dickinson, B.C., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• 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: 
  0.239 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors.

Osipiuk, J., Azizi, S.A., Dvorkin, S., Endres, M., Jedrzejczak, R., Jones, K.A., Kang, S., Kathayat, R.S., Kim, Y., Lisnyak, V.G., Maki, S.L., Nicolaescu, V., Taylor, C.A., Tesar, C., Zhang, Y.A., Zhou, Z., Randall, G., Michalska, K., Snyder, S.A., Dickinson, B.C., Joachimiak, A.

(2021) Nat Commun 12: 743-743

• PubMed: 33531496 
• DOI: https://doi.org/10.1038/s41467-021-21060-3
• Primary Citation Related Structures: 
  6WRH, 6WZU, 6XG3, 7JIR, 7JIT, 7JIV, 7JIW


• PubMed Abstract: 
  

  The pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to expand. Papain-like protease (PLpro) is one of two SARS-CoV-2 proteases potentially targetable with antivirals. PLpro is an attractive target because it plays an essential role in cleavage and maturation of viral polyproteins, assembly of the replicase-transcriptase complex, and disruption of host responses. We report a substantive body of structural, biochemical, and virus replication studies that identify several inhibitors of the SARS-CoV-2 enzyme. We determined the high resolution structure of wild-type PLpro, the active site C111S mutant, and their complexes with inhibitors. This collection of structures details inhibitors recognition and interactions providing fundamental molecular and mechanistic insight into PLpro. All compounds inhibit the peptidase activity of PLpro in vitro, some block SARS-CoV-2 replication in cell culture assays. These findings will accelerate structure-based drug design efforts targeting PLpro to identify high-affinity inhibitors of clinical value.

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Organizational Affiliation: 
• Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA.
Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA.
Department of Chemistry, University of Chicago, Chicago, IL, USA.
Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA.
Department of Chemistry, University of Chicago, Chicago, IL, USA. [e-mail].
Department of Chemistry, University of Chicago, Chicago, IL, USA. [e-mail].
Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA. [e-mail].
Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA. [e-mail].
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 36.9 kDa 
• Atom Count: 2,505 
• Modeled Residue Count: 305 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease	A	318	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  EC: 3.4.22
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VBY (Subject of Investigation/LOI)	B [auth A]	5-(acryloylamino)-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide C23 H22 N2 O2 QMJFETCLZITVFG-MRXNPFEDSA-N
MES	K [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	G [auth A], H [auth A], I [auth A], J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.239 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m37jiw

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.648	α = 90
b = 113.648	β = 90
c = 220.574	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-08-05 
Deposition Author(s): Osipiuk, J., Tesar, C., Endres, M., Lisnyak, V., Maki, S., Taylor, C., Zhang, Y., Zhou, Z., Azizi, S.A., Jones, K., Kathayat, R., Snyder, S.A., Dickinson, B.C., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2020-08-05
  Type: Initial release
  
• Version 1.1: 2021-01-27
  Changes: Structure summary
• Version 1.2: 2021-02-10
  Changes: Database references
• Version 1.3: 2021-03-31
  Changes: Structure summary
• Version 1.4: 2023-10-18
  Changes: Data collection, Database references, Refinement description