8CAC | pdb_00008cac

Crystal structure of SARS-CoV-2 Mpro-H172Y mutant in complex with 13b-K

PDB DOI: https://doi.org/10.2210/pdb8CAC/pdb

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

Deposited: 2023-01-24 Released: 2024-08-07
Deposition Author(s): Ibrahim, M., El Kilani, H., Hilgenfeld, R.
Funding Organization(s): European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free:
0.272 (Depositor), 0.278 (DCC)
R-Value Work:
0.212 (Depositor), 0.225 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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: 67.98 kDa
Atom Count: 4,883
Modeled Residue Count: 603
Deposited Residue Count: 604
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A [auth AAA], B [auth BBB]	302	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 D [auth BBB] SDF format, chain C [auth AAA] MOL2 format, chain D [auth BBB] MOL2 format, chain C [auth AAA] mmCIF format, chain D [auth BBB] mmCIF format, chain C [auth AAA]	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]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth BBB] MOL2 format, chain E [auth BBB] mmCIF format, chain E [auth BBB]	E [auth BBB]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth BBB] Interactions & Density Focus chain E [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.272 (Depositor), 0.278 (DCC)
R-Value Work: 0.212 (Depositor), 0.225 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.032	α = 90
b = 101.709	β = 90
c = 103.205	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

Funding Organization	Location	Grant Number
European Commission	European Union	--

Revision History (Full details and data files)

Version 1.0: 2024-08-07
Type: Initial release
Version 1.1: 2024-10-09
Changes: Structure summary
Version 1.2: 2025-09-03
Changes: Database references

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.