9IRA | pdb_00009ira

IBV 3CL protease (3CLpro) in complex with compound 6

PDB DOI: https://doi.org/10.2210/pdb9IRA/pdb

Classification: VIRAL PROTEIN
Organism(s): Avian infectious bronchitis virus (strain Beaudette)
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-07-15 Released: 2025-12-24
Deposition Author(s): Nie, T.Q., Su, H.X., Li, M.J., Xu, Y.C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.254 (Depositor), 0.253 (DCC)
R-Value Work:
0.225 (Depositor), 0.225 (DCC)
R-Value Observed:
0.226 (Depositor)

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

Structure-Based Development of Ultra-Broad-Spectrum 3C-Like Protease Inhibitors.

Su, H., Nie, T., Chen, G., Xiong, M., Zhang, Y., Wu, G., You, M., Xie, H., He, J., Xiong, Y., Hu, H., Zhao, W., Li, M., Xiao, G., Zhang, L., Xu, Y.

(2026) Adv Sci (Weinh) 13: e12342-e12342

PubMed: 41388583 Search on PubMed
DOI: https://doi.org/10.1002/advs.202512342
Primary Citation Related Structures:
9IR8, 9IR9, 9IRA, 9UOP, 9UOQ, 9UOR, 9UOS, 9X7D, 9X7E, 9X7F, 9X7G, 9X7H, 9X7I

PubMed Abstract:
Recurrence of coronavirus outbreaks and zoonotic origins of human coronaviruses underscore the importance of developing pan-coronavirus antivirals. The highly conserved 3C-like protease (3CL ^pro) in coronaviruses, together with the well-established druggability, makes it an ideal target for broad-spectrum antiviral therapeutics. Here, the inhibitory activity of approved 3CL ^pro inhibitors, including nirmatrelvir, ensitrelvir, and simnotrelvir, against fifteen 3CL ^pros is first reported by enzymatic assays. Despite their potent inhibition toward 3CL ^pros of β-CoVs, these inhibitors show reduced potency against 3CL ^pros from the other three genera, particularly against two newly identified human coronaviruses (α-CCoV-HuPn-2018 and δ-PDCoV). In this context, continued efforts in structure-based optimization of nirmatrelvir lead to the identification of compound 8 that potently inhibits a panel of 32 3CL ^pros across all subgenera (IC ₅₀s: 19-146 nm), with an IC ₅₀ value of 61 and 81 nm against α-CCoV-HuPn-2018 and δ-PDCoV 3CL ^pros, respectively. Moreover, it effectively inhibits nirmatrelvir-resistant 3CL ^pro mutants and demonstrates broad-spectrum antiviral efficacy in cells. These findings suggest an important rule that a small, non-cyclic P2 segment and a P4 segment with a suitable size are preferred by the design of ultra-broad-spectrum 3CL ^pro inhibitors, and provide a proof-of-concept guide for developing broad-spectrum antivirals as potential pan-CoV therapeutics.

Organizational Affiliation

State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.

Macromolecule Content

Total Structure Weight: 67.92 kDa
Atom Count: 4,866
Modeled Residue Count: 599
Deposited Residue Count: 614
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	307	Avian infectious bronchitis virus (strain Beaudette)	Mutation(s): 0 Gene Names: 1a EC: 3.4.22
UniProt
Find proteins for P0C6V3 (Avian infectious bronchitis virus (strain Beaudette)) Explore P0C6V3 Go to UniProtKB: P0C6V3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C6V3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1D7M (Subject of Investigation/LOI) Query on A1D7M Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	(2~{S})-~{N}-[(2~{S})-1-azanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[(2~{S})-3,3-dimethyl-2-(methylsulfonylamino)butanoyl]amino]-4-methyl-pentanamide C₂₀ H₃₇ N₅ O₅ S ZAOOYQOECLDTAP-ATAPGNLGSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]