8Y4H | pdb_00008y4h

Experimental Data Snapshot

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

(2025) Commun Biol 8: 493-493

PubMed: 40133408 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s42003-025-07929-9
Primary Citation of Related Structures:
8Y4G, 8Y4H, 8YWY, 8YWZ, 9INL, 9INM, 9LUF, 9LUG

PubMed Abstract:
The COVID-19 pandemic has caused significant global health and economic disruption. Mutations E166N, E166R, E166N, S144A and His163A in the SARS-CoV-2 main protease (M ^pro) have been implicated in reducing the efficacy of certain antiviral treatments. Bofutrelvir, a promising inhibitor, has shown effectiveness against SARS-CoV-2 M ^pro. This study aims to evaluate the inhibitory effects of Bofutrelvir on the E166N, E166R, His163A, E166V and S144A mutants of SARS-CoV-2 M ^pro, as well as on MERS-CoV M ^pro. Our findings indicate a substantial reduction in the inhibitory potency of Bofutrelvir against these mutants and MERS-CoV, with IC ₅₀ values significantly higher than those for the wild-type SARS-CoV-2 M ^pro. Specifically, the E166N, E166R, E166V, S144A, and H163A mutations significantly reduce the binding affinity and inhibitory effectiveness of Bofutrelvir due to disrupted hydrogen bonds, altered binding site stability, and reduced enzyme activity. Structural analysis of the crystal complexes showed that changes in interactions at the S1 subsite in the mutants and the loss of hydrogen bonds at the S4 subsite in MERS-CoV M ^pro are critical factors contributing to the diminished inhibitory activity. These insights reveal the necessity of ongoing structural analysis to adapt therapeutic strategies.

Organizational Affiliation

Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China.

Macromolecule Content

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, B	301	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% 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
FHR (Subject of Investigation/LOI) Query on FHR 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]	~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide C₂₅ H₃₂ N₄ O₄ HPKJGHVHQWJOOT-ZJOUEHCJSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002347 (FHR) Query on PRD_002347	C [auth A], D [auth B]	~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide	Peptide-like / Inhibitor		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]