7VTH | pdb_00007vth

The crystal structure of SARS-CoV-2 3CL protease in complex with compound 1

• PDB DOI: https://doi.org/10.2210/pdb7VTH/pdb

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


• Deposited: 2021-10-29 Released: 2022-04-06 
• Deposition Author(s): Yamamoto, S., Tachibana, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.257 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.205 (Depositor) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Discovery of S-217622, a Noncovalent Oral SARS-CoV-2 3CL Protease Inhibitor Clinical Candidate for Treating COVID-19.

Unoh, Y., Uehara, S., Nakahara, K., Nobori, H., Yamatsu, Y., Yamamoto, S., Maruyama, Y., Taoda, Y., Kasamatsu, K., Suto, T., Kouki, K., Nakahashi, A., Kawashima, S., Sanaki, T., Toba, S., Uemura, K., Mizutare, T., Ando, S., Sasaki, M., Orba, Y., Sawa, H., Sato, A., Sato, T., Kato, T., Tachibana, Y.

(2022) J Med Chem 65: 6499-6512

• PubMed: 35352927 
• DOI: https://doi.org/10.1021/acs.jmedchem.2c00117
• Primary Citation Related Structures: 
  7VTH, 7VU6


• PubMed Abstract: 
  

  The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in millions of deaths and threatens public health and safety. Despite the rapid global spread of COVID-19 vaccines, effective oral antiviral drugs are urgently needed. Here, we describe the discovery of S-217622 , the first oral noncovalent, nonpeptidic SARS-CoV-2 3CL protease inhibitor clinical candidate. S-217622 was discovered via virtual screening followed by biological screening of an in-house compound library, and optimization of the hit compound using a structure-based drug design strategy. S-217622 exhibited antiviral activity in vitro against current outbreaking SARS-CoV-2 variants and showed favorable pharmacokinetic profiles in vivo for once-daily oral dosing. Furthermore, S-217622 dose-dependently inhibited intrapulmonary replication of SARS-CoV-2 in mice, indicating that this novel noncovalent inhibitor could be a potential oral agent for treating COVID-19.

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Organizational Affiliation: 
• Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan.
International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan.

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 69.85 kDa 
• Atom Count: 4,737 
• Modeled Residue Count: 599 
• Deposited Residue Count: 622 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	311	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
7XB (Subject of Investigation/LOI)	C [auth A], D [auth B]	2-[4-[[4-[bis(fluoranyl)methoxy]-2-methyl-phenyl]amino]-2,6-bis(oxidanylidene)-3-[[3,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazin-1-yl]-N-methyl-ethanamide C21 H18 F5 N5 O4 JHDIUUFGPILEJO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.257 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.205 (Depositor) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.411	α = 90
b = 54.27	β = 99.42
c = 114.497	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
CrysalisPro	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-04-06 
Deposition Author(s): Yamamoto, S., Tachibana, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-04-06
  Type: Initial release
  
• Version 1.1: 2022-04-13
  Changes: Database references
• Version 1.2: 2022-05-25
  Changes: Database references
• Version 1.3: 2023-11-29
  Changes: Data collection, Refinement description