9LVT | pdb_00009lvt

Crystal structure of SARS-CoV-2 3CL protease in complex with compound 4

• PDB DOI: https://doi.org/10.2210/pdb9LVT/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: 
  0.237 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.197 (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, O., Tanimura, M., Dodo, R., Maruyama, Y., Sawa, H., Watari, R., Miyano, T., Kato, T., Sato, T., Tachibana, Y.

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 68.95 kDa 
• Atom Count: 4,840 
• Modeled Residue Count: 593 
• Deposited Residue Count: 616 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	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
A1L7Q (Subject of Investigation/LOI)	C [auth A], D [auth B]	1-(2-azanylideneethyl)-6-(1,3-dihydroisoindol-2-yl)-3-(5-methylpyridin-3-yl)-5-[[3,4,5-tris(fluoranyl)phenyl]methyl]pyrimidine-2,4-dione C27 H22 F3 N5 O2 XJHRRUKAUCQCNU-SVRKQYBGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.237 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.013	α = 90
b = 99.052	β = 108.16
c = 58.765	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