7V1T

A dual Inhibitor Against Main Protease

• PDB DOI: https://doi.org/10.2210/pdb7V1T/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2021-08-06 Released: 2022-08-10 
• Deposition Author(s): Yu, W.Y., Xiao, Y.B., Zhao, Y.C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 0.245 
• R-Value Work: 0.186 
• R-Value Observed: 0.192 

Literature

SARS-CoV-2 Mpro complex with inhibitor

Yu, W.Y., Xiao, Y.B., Zhao, Y.C., Lai, M.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 34.24 kDa 
• Atom Count: 2,386 
• Modelled Residue Count: 305 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  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
5IL (Subject of Investigation/LOI)	B [auth A]	5,8-bis(oxidanylidene)-7-[(2-piperazin-1-ylphenyl)amino]naphthalene-1-sulfonamide C20 H20 N4 O4 S JAMVFKPFIUKEMG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 0.245 
• R-Value Work: 0.186 
• R-Value Observed: 0.192 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.03	α = 90
b = 53.68	β = 101.68
c = 44.86	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-10 
Deposition Author(s): Yu, W.Y., Xiao, Y.B., Zhao, Y.C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	C060301

Revision History  

• Version 1.0: 2022-08-10
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description