8BFO | pdb_00008bfo

Structure of the apo form of Mpro from SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb8BFO/pdb

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


• Deposited: 2022-10-26 Released: 2023-11-08 
• Deposition Author(s): Medrano, F.J., Romero, A.
• Funding Organization(s): Other government

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.286 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.221 (DCC) 

Starting Model: experimental

Literature

Peptidyl nitroalkene inhibitors of main protease rationalized by computational and crystallographic investigations as antivirals against SARS-CoV-2.

Medrano, F.J., de la Hoz-Rodriguez, S., Marti, S., Arafet, K., Schirmeister, T., Hammerschmidt, S.J., Muller, C., Gonzalez-Martinez, A., Santillana, E., Ziebuhr, J., Romero, A., Zimmer, C., Weldert, A., Zimmermann, R., Lodola, A., Swiderek, K., Moliner, V., Gonzalez, F.V.

(2024) Commun Chem 7: 15-15

• PubMed: 38238420 
• DOI: https://doi.org/10.1038/s42004-024-01104-7
• Primary Citation Related Structures: 
  8BFO, 8BFQ, 8BGA, 8BGD


• PubMed Abstract: 
  

  The coronavirus disease 2019 (COVID-19) pandemic continues to represent a global public health issue. The viral main protease (M ^pro ) represents one of the most attractive targets for the development of antiviral drugs. Herein we report peptidyl nitroalkenes exhibiting enzyme inhibitory activity against M ^pro (K _i : 1-10 μM) good anti-SARS-CoV-2 infection activity in the low micromolar range (EC ₅₀ : 1-12 μM) without significant toxicity. Additional kinetic studies of compounds FGA145, FGA146 and FGA147 show that all three compounds inhibit cathepsin L, denoting a possible multitarget effect of these compounds in the antiviral activity. Structural analysis shows the binding mode of FGA146 and FGA147 to the active site of the protein. Furthermore, our results illustrate that peptidyl nitroalkenes are effective covalent reversible inhibitors of the M ^pro and cathepsin L, and that inhibitors FGA145, FGA146 and FGA147 prevent infection against SARS-CoV-2.

---

Organizational Affiliation: 
• Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain. [e-mail].
Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12071, Castelló, Spain.
Departament de Química Física i Analítica, Universitat Jaume I, 12071, Castelló, Spain.
Institute of Pharmaceutical and BiomedicalSciences, Johannes Gutenberg-University Mainz, Staudinger Weg 5, 55128, Mainz, Germany.
Institute of Medical Virology, Justus Liebig University Giessen, Schubertstrasse 81, 35392, Giessen, Germany.
Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parma, Italy.
Departament de Química Física i Analítica, Universitat Jaume I, 12071, Castelló, Spain. [e-mail].
Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12071, Castelló, Spain. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 33.7 kDa 
• Atom Count: 2,418 
• Modeled Residue Count: 305 
• Deposited Residue Count: 305 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	305	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.286 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.221 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.98	α = 90
b = 53.933	β = 101.004
c = 44.738	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-08 
Deposition Author(s): Medrano, F.J., Romero, A.

---

Funding Organization	Location	Grant Number
Other government	Spain	PIE-202020E224

Revision History  

• Version 1.0: 2023-11-08
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Database references, Structure summary
• Version 1.2: 2026-03-04
  Changes: Refinement description