8RI4

Crystal structure of the SARS-CoV-2 Main Protease inhibited by (2-methylsulfanyl-6,7-dihydro-[1,4]dioxino[2,3-f]benzimidazol-3-yl)-(p-tolyl)methanone

• PDB DOI: https://doi.org/10.2210/pdb8RI4/pdb

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


• Deposited: 2023-12-18 Released: 2025-01-01 
• Deposition Author(s): Charton, J., Deprez, B., Hanoulle, X.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.234 
• R-Value Work: 0.189 

Starting Model: experimental

Literature

Crystal structure of the SARS-CoV-2 Main Protease inhibited by (2-methylsulfanyl-6,7-dihydro-[1,4]dioxino[2,3-f]benzimidazol-3-yl)-(p-tolyl)methanone

Charton, J., Hanoulle, X., Deprez, B.

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 34.34 kDa 
• Atom Count: 2,629 
• Modelled Residue Count: 301 
• 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4MA (Subject of Investigation/LOI)	B [auth A]	4-METHYLBENZOIC ACID C8 H8 O2 LPNBBFKOUUSUDB-UHFFFAOYSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
FMT	F [auth A], G [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.234 
• R-Value Work: 0.189 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.247	α = 90
b = 54.004	β = 101.142
c = 44.68	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
MOLREP	phasing
Aimless	data scaling
XDS	data reduction
MxCuBE	data collection

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-01 
Deposition Author(s): Charton, J., Deprez, B., Hanoulle, X.

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Funding Organization	Location	Grant Number
Other government	France	3CLPRO-SCREEN-NMR
Other government	France	ERDF REACT-EU (convention 22003061)

Revision History  

• Version 1.0: 2025-01-01
  Type: Initial release