8DPR

Crystal structure of SARS-CoV-2 main protease in complex with inhibitor TKB-248

PDB DOI: https://doi.org/10.2210/pdb8DPR/pdb

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

Deposited: 2022-07-16 Released: 2022-08-24
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: 2.00 Å
R-Value Free: 0.247
R-Value Work: 0.190
R-Value Observed: 0.193

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 34.22 kDa
Atom Count: 2,398
Modelled Residue Count: 303
Deposited Residue Count: 303
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T43 (Subject of Investigation/LOI) Query on T43 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2,2,2-trifluoro-N-{(2S)-1-[(1R,2S,5S)-2-({(2S)-1-(4-fluoro-1,3-benzothiazol-2-yl)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamothioyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexan-3-yl]-3,3-dimethyl-1-oxobutan-2-yl}acetamide C₃₀ H₃₅ F₄ N₅ O₄ S₂ GDKLDALGJZVEKT-MCUUEWDYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.247
R-Value Work: 0.190
R-Value Observed: 0.193
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.403	α = 90
b = 53.926	β = 101.63
c = 45.678	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2022-08-24
Type: Initial release
Version 2.0: 2022-12-07
Type: Coordinate replacement
Reason: Ligand geometry
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
Version 2.1: 2023-09-06
Changes: Data collection, Database references
Version 2.2: 2023-10-25
Changes: Refinement description