9NWB | pdb_00009nwb

Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-280-5I

• PDB DOI: https://doi.org/10.2210/pdb9NWB/pdb

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


• Deposited: 2025-03-21 Released: 2025-06-04 
• Deposition Author(s): Bulut, H., Hayashi, H., Hattori, S., Li, M., Das, D., 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: 2.01 Å
• R-Value Free: 
  0.248 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Impact of Single Halogen Atom Substitutions on Antiviral Profile of Inhibitors Targeting SARS-CoV‐2 Main Protease.

Bulut, H., Higashi-Kuwata, N., Ogata-Aoki, H., Hayashi, H., Takamune, N., Kishimoto, N., Das, D., Li, M., Wlodawer, A., Misumi, S., Tamamura, H., Mitsuya, H.

(2026) ACS Omega 11: 4541-4550

• PubMed: 41626465 
• DOI: https://doi.org/10.1021/acsomega.5c10895
• Primary Citation of Related Structures:  
  9NWA, 9NWB, 9NWC


• PubMed Abstract: 
  

  The SARS-CoV-2 main protease (M ^pro ) remains a prime antiviral target because its inhibition halts viral replication. To probe how subtle atomic changes influence drug performance, we carried out a systematic halogen scan on a potent ketoamide scaffold, replacing a single fluorine with chlorine, bromine, or iodine. Enzymatic assays revealed that the F- and Cl-substituted analogues inhibit M ^pro at nanomolar levels, whereas Br and I variants are 10- to 20-fold weaker. Cell-based antiviral tests mirrored this trend, yet uptake studies showed the opposite: iodine markedly enhances intracellular accumulation. High-resolution X-ray structures (1.6-1.8 Å) explain the dichotomy: small halogens fit snugly in the S1' σ-hole pocket, maximizing hydrogen-bond geometry, while bulkier atoms distort binding but create a lipophilic patch that boosts permeability. These data yield the first fluorine-to-iodine structure-activity map for SARS-CoV-2 M ^pro inhibitors. These findings highlight the critical role of halogen selection in antiviral inhibitor design.

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Organizational Affiliation: 
• Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, NIH, Bethesda, Maryland 20892, United States.
Department of Refractory Viral Diseases, National Institute of Global Health and Medicine, Japan Institute for Health Security, Tokyo 162-8655, Japan.
Division of Hematopoiesis, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-8556, Japan.
International Research Institute of Disaster Science, Tohoku University, Miyagi 980-8575, Japan.
Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan.
Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States.
Laboratory of Cell Biology, National Cancer Institute, Bethesda, Maryland 20892, United States.
Department of Medicinal Chemistry, Laboratory for Biomaterials and Bioengineering, Institute of Integrated Research, Institute of Science Tokyo, Tokyo 101-0062, Japan.
Kumamoto University Hospital, Kumamoto 860-8556, 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: 34.59 kDa 
• Atom Count: 2,436 
• Modeled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF1a polyprotein	A	306	Severe acute respiratory syndrome coronavirus	Mutation(s): 0  Gene Names: ORF1ab
UniProt
Find proteins for A0A8B1JK87 (Severe acute respiratory syndrome coronavirus 2) Explore A0A8B1JK87  Go to UniProtKB:  A0A8B1JK87

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1B7A	B [auth A]	(1R,2S,5S)-N-{(1S,2R)-1-hydroxy-1-(5-iodo-1,3-benzothiazol-2-yl)-3-[(3R)-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 F3 I N5 O5 S AMWSCQMTJKQAAP-XSQCLQQESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.248 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.412	α = 90
b = 64.071	β = 90
c = 104.988	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-04 
Deposition Author(s): Bulut, H., Hayashi, H., Hattori, S., Li, M., Das, D., 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
  
• Version 1.1: 2026-02-18
  Changes: Database references