9LVV | pdb_00009lvv

Crystal structure of SARS-CoV-2 3CL protease in complex with compound 17 (S-892216)

• PDB DOI: https://doi.org/10.2210/pdb9LVV/pdb

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


• Deposited: 2025-02-12 Released: 2025-05-14 
• Deposition Author(s): Unoh, Y., Hirai, K., Uehara, S., Kawashima, S., Nobori, H., Sato, J., Shibayama, H., Hori, A., Nakahara, K., Kurahashi, K., Takamatsu, M., Yamamoto, S., Zhang, O., Tanimura, M., Dodo, R., Maruyama, Y., Sawa, H., Watari, R., Miyano, T., Kato, T., Sato, T., Tachibana, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.242 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Discovery of the Clinical Candidate S-892216 : A Second-Generation of SARS-CoV-2 3CL Protease Inhibitor for Treating COVID-19.

Unoh, Y., Hirai, K., Uehara, S., Kawashima, S., Nobori, H., Sato, J., Shibayama, H., Hori, A., Nakahara, K., Kurahashi, K., Takamatsu, M., Yamamoto, S., Zhang, Q., Tanimura, M., Dodo, R., Maruyama, Y., Sawa, H., Watari, R., Miyano, T., Kato, T., Sato, T., Tachibana, Y.

(2025) J Med Chem 68: 21099-21119

• PubMed: 40616520 
• DOI: https://doi.org/10.1021/acs.jmedchem.5c00754
• Primary Citation of Related Structures:  
  9LVR, 9LVT, 9LVV


• PubMed Abstract: 
  

  The coronavirus disease 2019 (COVID-19) pandemic crisis has been mitigated by worldwide efforts to develop vaccines and therapeutic drugs. However, there remains concern regarding public health and an unmet need for therapeutic options. Herein, we report the discovery of S-892216 , a second-generation SARS-CoV-2 3C-like protease (3CL ^pro ) inhibitor, to treat COVID-19. S-892216 is a reversible covalent 3CL ^pro inhibitor with highly potent antiviral activity and an EC ₅₀ value of 2.48 nM against SARS-CoV-2 infected cells. Structure-based design of a covalent modifier for compound 1 revealed that introducing a nitrile warhead increased 3CL ^pro inhibition activity by 180-fold. Subsequent optimization efforts yielded S-892216 , which combined a favorable pharmacokinetic profile and high off-target selectivity. S-892216 exhibited antiviral activity against diverse SARS-CoV-2 variants, including major mutations reducing antiviral activities of nirmatrelvir and ensitrelvir. In SARS-CoV-2-infected mice, S-892216 inhibited viral replication in the lungs similar to ensitrelvir, although at a 30-fold lower dose.

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Organizational Affiliation: 
• Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan.
Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo 001-0021, Japan.
International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan.
One Health Research Center, Hokkaido University, Sapporo 060-0818, Japan.
Global Virus Network, 12901 Bruce B. Downs Blvd. MDC02, Tampa, Florida 33612, United States.

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: 34.49 kDa 
• Atom Count: 2,464 
• Modeled Residue Count: 299 
• Deposited Residue Count: 308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	308	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  EC: 3.4.22.69
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1  Go to UniProtKB:  P0DTC1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L7R (Subject of Investigation/LOI)	B [auth A]	1-(2-azanylideneethyl)-6-[6,6-bis(fluoranyl)-2-azaspiro[3.3]heptan-2-yl]-5-(3-chloranyl-4-fluoranyl-phenyl)-3-(5-chloranylpyridin-3-yl)pyrimidine-2,4-dione C23 H18 Cl2 F3 N5 O2 RXJZRRLUUSKVDH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.242 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.455	α = 90
b = 53.73	β = 98.88
c = 114.307	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Unoh, Y., Hirai, K., Uehara, S., Kawashima, S., Nobori, H., Sato, J., Shibayama, H., Hori, A., Nakahara, K., Kurahashi, K., Takamatsu, M., Yamamoto, S., Zhang, O., Tanimura, M., Dodo, R., Maruyama, Y., Sawa, H., Watari, R., Miyano, T., Kato, T., Sato, T., Tachibana, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release
  
• Version 1.1: 2025-08-27
  Changes: Database references
• Version 1.2: 2025-11-05
  Changes: Database references