9NWC | pdb_00009nwc

Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-276-5Br

• PDB DOI: https://doi.org/10.2210/pdb9NWC/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-21 Released: 2025-06-04 
• Deposition Author(s): Bulut, H., Kuwata, N., Hayashi, H., Aoki, H., Hattori, S., Li, M., Das, D., Misumi, S., Wlodawer, A., 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: 1.79 Å
• R-Value Free: 
  0.227 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Impact of Single Halogen Atom Substitutions on Potency of Inhibitors Targeting SARS-CoV-2 Main Protease

Bulut, H., Kuwata, N., Hayashi, H., Aoki, H., Das, D., Mi, L., Wlodawer, A., 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)

Macromolecule Content 

• Total Structure Weight: 69.08 kDa 
• Atom Count: 4,944 
• Modeled Residue Count: 612 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	306	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1B7B	C [auth A], D [auth B]	(1R,2S,5S)-N-{(1S,2S)-1-(5-bromo-1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-D-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide C30 H37 Br F3 N5 O5 S BTXSNAHBFHGNCS-GOHKFJIPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.227 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.339	α = 68.31
b = 52.972	β = 87.69
c = 61.907	γ = 89.98

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-04 
Deposition Author(s): Bulut, H., Kuwata, N., Hayashi, H., Aoki, H., Hattori, S., Li, M., Das, D., Misumi, S., Wlodawer, A., 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: 2025-06-04
  Type: Initial release