9BSE | pdb_00009bse

Structure of the SARS-CoV-2 main protease in complex with inhibitor YR-B-165

PDB DOI: https://doi.org/10.2210/pdb9BSE/pdb

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

Deposited: 2024-05-13 Released: 2025-05-14
Deposition Author(s): Blankenship, L.R., Liu, W.R.
Funding Organization(s): Welch Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.239 (Depositor), 0.239 (DCC)
R-Value Work:
0.216 (Depositor), 0.216 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of the SARS-CoV-2 main protease

Blankenship, L.R., Liu, W.R.

To be published.

Macromolecule Content

Total Structure Weight: 34.36 kDa
Atom Count: 2,628
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
3C-like proteinase nsp5	A	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AR6 (Subject of Investigation/LOI) Query on A1AR6 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]	(3S)-N-{(2S)-1-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-2-[(2R)-3,3-dimethyl-2-(2,2,2-trifluoroacetamido)butanoyl]-2-azaspiro[4.5]decane-3-carboxamide C₂₅ H₄₀ F₃ N₅ O₄ MLNFOXDPMDRARB-XLAORIBOSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.239 (Depositor), 0.239 (DCC)
R-Value Work: 0.216 (Depositor), 0.216 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.636	α = 90
b = 80.773	β = 97
c = 89.275	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-14

Deposition Author(s):

Blankenship, L.R.

Funding Organization	Location	Grant Number
Welch Foundation	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-05-14
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.