8UH9

Crystal structure of SARS-CoV-2 main protease E166V mutant in complex with an inhibitor TKB-272

• PDB DOI: https://doi.org/10.2210/pdb8UH9/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-10-07 Released: 2023-12-20 
• Deposition Author(s): Bulut, H., Hayashi, H., Kuwata, N., Tsuji, K., Das, D., Tamamura, H., Mitsuya, H.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.240 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Starting Model: experimental

Literature

TKB272, an Orally Available SARS-CoV-2-Mpro Inhibitor Containing 5-Fluorobenzothiazole, Potently Blocks SARS-CoV-2 Replication without Ritonavir

Higashi-Kuwata, N., Bulut, H., Hayashi, H., Tsuji, K., Ogata-Aoki, H., Kiso, M., Takamune, N., Kishimoto, N., Hattori, S., Ishii, T., Kobayakawa, T., Nakano, K., Das, D., Saruwatari, J., Hasegawa, K., Murayama, K., Sukenaga, Y., Takamatsu, Y., Yoshimura, K., Aoki, M., Okamura, T., Yamayoshi, S., Kawaoka, Y., Misumi, S., Tamamura, H., Mitsuya, H.

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: 34.56 kDa 
• Atom Count: 2,421 
• Modelled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  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
WOK (Subject of Investigation/LOI)	B [auth A]	(1R,2S,5S)-N-{(1S,2S)-1-(5-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 AVAISVNJDSSFQV-UDQBHXPNSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.240 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.673	α = 90
b = 53.09	β = 101.96
c = 45.774	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-20 
Deposition Author(s): Bulut, H., Hayashi, H., Kuwata, N., Tsuji, K., Das, D., Tamamura, H., Mitsuya, H.

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

Revision History  

• Version 1.0: 2023-12-20
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary