8BGD

Structure of Mpro from SARS-CoV-2 in complex with FGA147

• PDB DOI: https://doi.org/10.2210/pdb8BGD/pdb

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


• Deposited: 2022-10-27 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: 1.62 Å
• R-Value Free: 0.244 
• R-Value Work: 0.191 

Literature

Peptidyl Nitroalkenes Inhibit SARS-CoV-2 Main Protease and Block Virus Replication

Medrano, F.J., Romero, A.

To be published.

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: 34.27 kDa 
• Atom Count: 2,572 
• Modelled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	306	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QH0 (Subject of Investigation/LOI)	B [auth A]	(phenylmethyl) N-[(2S)-4-methyl-1-[[(2S)-4-nitro-1-[(3R)-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]amino]-1-oxidanylidene-pentan-2-yl]carbamate C22 H32 N4 O6 AHDULYSHSMKYBB-QRVBRYPASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.244 
• R-Value Work: 0.191 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.721	α = 90
b = 62.661	β = 90
c = 106.128	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