7OFU

Structure of SARS-CoV-2 Papain-like protease PLpro in complex with 3, 4-Dihydroxybenzoic acid, methyl ester


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.175 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 3.3 of the entry. See complete history


Literature

Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease.

Srinivasan, V.Brognaro, H.Prabhu, P.R.de Souza, E.E.Gunther, S.Reinke, P.Y.A.Lane, T.J.Ginn, H.Han, H.Ewert, W.Sprenger, J.Koua, F.H.M.Falke, S.Werner, N.Andaleeb, H.Ullah, N.Franca, B.A.Wang, M.Barra, A.L.C.Perbandt, M.Schwinzer, M.Schmidt, C.Brings, L.Lorenzen, K.Schubert, R.Machado, R.R.G.Candido, E.D.Oliveira, D.B.L.Durigon, E.L.Niebling, S.Garcia, A.S.Yefanov, O.Lieske, J.Gelisio, L.Domaracky, M.Middendorf, P.Groessler, M.Trost, F.Galchenkova, M.Mashhour, A.R.Saouane, S.Hakanpaa, J.Wolf, M.Alai, M.G.Turk, D.Pearson, A.R.Chapman, H.N.Hinrichs, W.Wrenger, C.Meents, A.Betzel, C.

(2022) Commun Biol 5: 805-805

  • DOI: https://doi.org/10.1038/s42003-022-03737-7
  • Primary Citation of Related Structures:  
    7NFV, 7OFS, 7OFT, 7OFU

  • PubMed Abstract: 

    SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, facilitating cleavage of the viral polypeptide chain, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to support coronaviruses in evading the host's innate immune responses. We identified three phenolic compounds bound to PLpro, preventing essential molecular interactions to ISG15 by screening a natural compound library. The compounds identified by X-ray screening and complexed to PLpro demonstrate clear inhibition of PLpro in a deISGylation activity assay. Two compounds exhibit distinct antiviral activity in Vero cell line assays and one inhibited a cytopathic effect in non-cytotoxic concentration ranges. In the context of increasing PLpro mutations in the evolving new variants of SARS-CoV-2, the natural compounds we identified may also reinstate the antiviral immune response processes of the host that are down-regulated in COVID-19 infections.


  • Organizational Affiliation

    Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany. vasundara.srinivasan@chemie.uni-hamburg.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Papain-like protease nsp3A [auth AAA]315Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC1 
Go to UniProtKB:  P0DTC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HE9 (Subject of Investigation/LOI)
Query on HE9

Download Ideal Coordinates CCD File 
B [auth AAA]methyl 3,4-bis(oxidanyl)benzoate
C8 H8 O4
CUFLZUDASVUNOE-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth AAA],
G [auth AAA],
H [auth AAA],
I [auth AAA]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth AAA],
D [auth AAA]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth AAA]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth AAA]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.175 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.391α = 90
b = 82.391β = 90
c = 134.132γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyEXC 2056 - project ID 390715994
European CommissionEuropean UnionEU project 101003551 - EXSCALATE4CoV (E4C)

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 2.0: 2021-11-24
    Type: Coordinate replacement
    Reason: Model orientation/position
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 3.0: 2022-04-13
    Type: Coordinate replacement
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Experimental preparation, Refinement description, Source and taxonomy, Structure summary
  • Version 3.1: 2022-09-07
    Changes: Database references
  • Version 3.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 3.3: 2024-09-18
    Changes: Derived calculations