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

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

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This is version 1.4 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41467-021-21060-3
  • Primary Citation of 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.

  • Organizational Affiliation

    Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Papain-like protease318Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
EC: 3.4.22
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VBY (Subject of Investigation/LOI)
Query on VBY

Download Ideal Coordinates CCD File 
B [auth A]5-(acryloylamino)-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide
C23 H22 N2 O2
Query on MES

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C6 H13 N O4 S
Query on ZN

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C [auth A],
D [auth A],
E [auth A],
F [auth A]
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A]
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.648α = 90
b = 113.648β = 90
c = 220.574γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700060C

Revision History  (Full details and data files)

  • 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