8DOX

Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-245

• PDB DOI: https://doi.org/10.2210/pdb8DOX/pdb

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


• Deposited: 2022-07-14 Released: 2022-09-21 
• Deposition Author(s): Bulut, H., Hayashi, H., Tsuji, K., Kuwata, N., Das, D., Tamamura, H., Mitsuya, H.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.229 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Literature

Identification of SARS-CoV-2 M pro inhibitors containing P1' 4-fluorobenzothiazole moiety highly active against SARS-CoV-2.

Higashi-Kuwata, N., Tsuji, K., Hayashi, H., Bulut, H., Kiso, M., Imai, M., Ogata-Aoki, H., Ishii, T., Kobayakawa, T., Nakano, K., Takamune, N., Kishimoto, N., Hattori, S.I., Das, D., Uemura, Y., Shimizu, Y., Aoki, M., Hasegawa, K., Suzuki, S., Nishiyama, A., Saruwatari, J., Shimizu, Y., Sukenaga, Y., Takamatsu, Y., Tsuchiya, K., Maeda, K., Yoshimura, K., Iida, S., Ozono, S., Suzuki, T., Okamura, T., Misumi, S., Kawaoka, Y., Tamamura, H., Mitsuya, H.

(2023) Nat Commun 14: 1076-1076

• PubMed: 36841831 
• DOI: https://doi.org/10.1038/s41467-023-36729-0
• Primary Citation of Related Structures:  
  8DOX, 8DPR


• PubMed Abstract: 
  

  COVID-19 caused by SARS-CoV-2 has continually been serious threat to public health worldwide. While a few anti-SARS-CoV-2 therapeutics are currently available, their antiviral potency is not sufficient. Here, we identify two orally available 4-fluoro-benzothiazole-containing small molecules, TKB245 and TKB248, which specifically inhibit the enzymatic activity of main protease (M ^pro ) of SARS-CoV-2 and significantly more potently block the infectivity and replication of various SARS-CoV-2 strains than nirmatrelvir, molnupiravir, and ensitrelvir in cell-based assays employing various target cells. Both compounds also block the replication of Delta and Omicron variants in human-ACE2-knocked-in mice. Native mass spectrometric analysis reveals that both compounds bind to dimer M ^pro , apparently promoting M ^pro dimerization. X-ray crystallographic analysis shows that both compounds bind to M ^pro 's active-site cavity, forming a covalent bond with the catalytic amino acid Cys-145 with the 4-fluorine of the benzothiazole moiety pointed to solvent. The data suggest that TKB245 and TKB248 might serve as potential therapeutics for COVID-19 and shed light upon further optimization to develop more potent and safer anti-SARS-CoV-2 therapeutics.

---

Organizational Affiliation: 

Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 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: 34.14 kDa 
• Atom Count: 2,505 
• Modelled Residue Count: 303 
• Deposited Residue Count: 303 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	303	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T2L (Subject of Investigation/LOI)	B [auth A]	(1R,2S,5S)-N-{(1S,2S)-1-(4-fluoro-1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide C30 H37 F4 N5 O5 S HZJVVPOOURAASY-SWSSSNQJSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.229 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.333	α = 90
b = 52.913	β = 103.74
c = 45.604	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction
MOLREP	phasing
xia2	data reduction
DIALS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-21 
Deposition Author(s): Bulut, H., Hayashi, H., Tsuji, K., Kuwata, N., Das, D., Tamamura, H., Mitsuya, H.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2022-09-21
  Type: Initial release
  
• Version 1.1: 2023-09-06
  Changes: Data collection, Database references
• Version 1.2: 2023-10-18
  Changes: Refinement description