8B0S | pdb_00008b0s

SARS-COV-2 Main Protease adduct with Au(NHC)Cl


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 
    0.273 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.254 (Depositor), 0.254 (DCC) 
  • R-Value Observed: 
    0.255 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8B0S

This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7DAT

Literature

Gold-Based Metal Drugs as Inhibitors of Coronavirus Proteins: The Inhibition of SARS-CoV-2 Main Protease by Auranofin and Its Analogs.

Massai, L.Grifagni, D.De Santis, A.Geri, A.Cantini, F.Calderone, V.Banci, L.Messori, L.

(2022) Biomolecules 12

  • DOI: https://doi.org/10.3390/biom12111675
  • Primary Citation Related Structures: 
    8B0S, 8B0T

  • PubMed Abstract: 

    Gold compounds have a long tradition in medicine and offer many opportunities for new therapeutic applications. Herein, we evaluated the lead compound Auranofin and five related gold(I) complexes as possible inhibitors of SARS-CoV-2 Main Protease (SARS-CoV-2 M pro ), a validated drug target for the COVID-19 disease. The investigational panel of gold compounds included Auranofin; three halido analogues, i.e., Au(PEt 3 )Cl, Au(PEt 3 )Br, and Au(PEt 3 )I; and two gold carbene complexes, i.e., Au(NHC)Cl and [Au(NHC) 2 ]PF 6 . Notably, all these gold compounds, with the only exception of [Au(NHC) 2 ]PF 6 , turned out to be potent inhibitors of the catalytic activity of SARS-CoV-2 M pro : the measured K i values were in the range 2.1-0.4 μM. The reactions of the various gold compounds with SARS-CoV-2 M pro were subsequently investigated through electrospray ionization (ESI) mass spectrometry (MS) upon a careful optimization of the experimental conditions; the ESI MS spectra provided clear evidence for the formation of tight metallodrug-protein adducts and for the coordination of well defined gold-containing fragments to the SARS-CoV-2 M pro , again with the only exception of [Au(NHC) 2 ]PF 6 , The metal-protein stoichiometry was unambiguously determined for the resulting species. The crystal structures of the metallodrug- M pro adducts were solved in the case of Au(PEt 3 )Br and Au(NHC)Cl. These crystal structures show that gold coordination occurs at the level of catalytic Cys 145 in the case of Au(NHC)Cl and at the level of both Cys 145 and Cys 156 for Au(PEt 3 )Br. Tight coordination of gold atoms to functionally relevant cysteine residues is believed to represent the true molecular basis of strong enzyme inhibition.


  • Organizational Affiliation
    • Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019 Florence, Italy.

Macromolecule Content 

  • Total Structure Weight: 33.49 kDa 
  • Atom Count: 2,348 
  • Modeled Residue Count: 301 
  • Deposited Residue Count: 301 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5301Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
EC: 3.4.22.69
UniProt
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AU

Query on AU



Download:Ideal Coordinates CCD File
B [auth A]GOLD ION
Au
ZBKIUFWVEIBQRT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free:  0.273 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.254 (Depositor), 0.254 (DCC) 
  • R-Value Observed: 0.255 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.92α = 90
b = 53.27β = 102.85
c = 44.55γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Ministry of EducationItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description