9MCK | pdb_00009mck

Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with Leritrelvir

PDB DOI: https://doi.org/10.2210/pdb9MCK/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-03-17 Released: 2026-09-23
Deposition Author(s): Zhou, X.L., Li, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.228 (Depositor), 0.229 (DCC)
R-Value Work:
0.190 (Depositor), 0.191 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with Leritrelvir

Zhou, X.L., Li, J.

To be published.

Macromolecule Content

Total Structure Weight: 67.37 kDa
Atom Count: 4,923
Modeled Residue Count: 594
Deposited Residue Count: 596
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	298	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7ON (Subject of Investigation/LOI) Query on 7ON Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	Leritrelvir bound form C₃₁ H₄₆ F₃ N₅ O₆ FMXUVDFVVNRAMG-IFCRGVKQSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.228 (Depositor), 0.229 (DCC)
R-Value Work: 0.190 (Depositor), 0.191 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.357	α = 90
b = 97.374	β = 108.119
c = 58.284	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-09-23
Type: Initial release