23MD | pdb_000023md

Crystal structure of SARS-CoV-2 main protease M49I/M165I mutant in complex with leritrelvir

PDB DOI: https://doi.org/10.2210/pdb23MD/pdb

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

Deposited: 2026-02-11 Released: 2026-06-03
Deposition Author(s): Huang, X., Li, Q., Yang, Z., Zhong, N., Xiong, X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.219 (Depositor), 0.222 (DCC)
R-Value Work:
0.176 (Depositor), 0.183 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Enhanced Target Binding by Leritrelvir Restores Dimerization of M^pro Mutants and Mitigates Drug Resistance

Huang, X., Kuzmic, P., Zhang, S., Ramos-Guzman, C.A., Chen, X., Gui, J., Li, Q., Yan, S., Zou, B., Niu, C., Zhao, Y., Lin, H., Wang, N., Chen, J., Chen, X., Spencer, J., Mulholland, A.J., Chen, J., Zhong, N., Yang, Z., Xiong, X.

(2026) bioRxiv

DOI: https://doi.org/10.64898/2026.06.09.730104

Macromolecule Content

Total Structure Weight: 69.32 kDa
Atom Count: 5,376
Modeled Residue Count: 612
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 2 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EN0 (Subject of Investigation/LOI) Query on A1EN0 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	(3~{S},3~{a}~{S},6~{a}~{R})-2-[(2~{S})-2-cyclohexyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]ethanoyl]-~{N}-[(2~{S})-4-(cyclopentylamino)-3,4-bis(oxidanylidene)-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]-3,3~{a},4,5,6,6~{a}-hexahydro-1~{H}-cyclopenta[c]pyrrole-3-carboxamide C₃₁ H₄₄ F₃ N₅ O₆ ICGMMLTUQDVAST-HEZDJTGRSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B]	D [auth A], E [auth A], F [auth A], G [auth A], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B]