8C9O | pdb_00008c9o

Crystal structure of SARS-CoV-2 Mpro-S144A mutant in complex with 13b-K

PDB DOI: https://doi.org/10.2210/pdb8C9O/pdb

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

Deposited: 2023-01-23 Released: 2024-02-07
Deposition Author(s): Ibrahim, M., El Kilani, H., Hilgenfeld, R.
Funding Organization(s): European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free:
0.234 (Depositor), 0.240 (DCC)
R-Value Work:
0.198 (Depositor), 0.210 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

13b-K and Nirmatrelvir Resistance Mutations of SARS-CoV-2 Main Protease: Structural, Biochemical, and Biophysical Characterization of Free Enzymes and Inhibitor Complexes

El Kilani, H., Sun, X., Ibrahim, M.F., Curth, U., Hilgenfeld, R.

(2025) Crystals (Basel) 15

DOI: https://doi.org/10.3390/cryst15090758

Macromolecule Content

Total Structure Weight: 68.81 kDa
Atom Count: 5,104
Modeled Residue Count: 609
Deposited Residue Count: 612
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 [auth AAA], B [auth BBB]	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 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
O6K (Subject of Investigation/LOI) Query on O6K Download Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain D [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain D [auth BBB] mmCIF format, chain C [auth AAA] mmCIF format, chain D [auth BBB]	C [auth AAA], D [auth BBB]	~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate C₃₁ H₄₁ N₅ O₇ FRACPXUHUTXLCX-BELIEFIBSA-N		Interactions Focus chain C [auth AAA] Focus chain D [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain D [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.234 (Depositor), 0.240 (DCC)
R-Value Work: 0.198 (Depositor), 0.210 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.766	α = 90
b = 99.689	β = 90
c = 103.307	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	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: 2024-02-07

Deposition Author(s):

Funding Organization	Location	Grant Number
European Commission	European Union	--

Revision History (Full details and data files)

Version 1.0: 2024-02-07
Type: Initial release
Version 1.1: 2024-10-23
Changes: Structure summary
Version 1.2: 2025-09-03
Changes: Database references

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.