8DOX

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


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 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.3 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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5303Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T2L (Subject of Investigation/LOI)
Query on T2L

Download Ideal Coordinates CCD File 
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
Query on DMS

Download Ideal Coordinates CCD File 
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 = 115.333α = 90
b = 52.913β = 103.74
c = 45.604γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction
MOLREPphasing
xia2data reduction
DIALSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted T2LClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-10-23
    Changes: Structure summary