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)

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
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

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

Hattori, S., Bulut, H., Hayashi, H., Aoki, H., Kuwata, N., Das, D., Mi, L., Wlodawer, A., Misumi, S., Tamamura, H., Mitsuya, H.

To be published.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8B1JK87
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1B7A Query on A1B7A 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]	(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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-04

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: 2025-06-04
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.