8IG8

Crystal structure of SARS-Cov-2 main protease S46F mutant in complex with GC376

PDB DOI: https://doi.org/10.2210/pdb8IG8/pdb

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

Deposited: 2023-02-20 Released: 2024-03-06
Deposition Author(s): Zeng, X.Y., Zhang, J., Li, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.234
R-Value Work: 0.204
R-Value Observed: 0.205

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

Structural Basis for Coronaviral Main Proteases Inhibition by the 3CLpro Inhibitor GC376.

Lin, C., Zhu, Z., Jiang, H., Zou, X., Zeng, X., Wang, J., Zeng, P., Li, W., Zhou, X., Zhang, J., Wang, Q., Li, J.

(2024) J Mol Biol 436: 168474-168474

PubMed: 38311236 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2024.168474
Primary Citation of Related Structures:
8IG4, 8IG5, 8IG6, 8IG7, 8IG8, 8IG9, 8IGA, 8IGB

PubMed Abstract:
The main protease (M ^pro) of coronaviruses participates in viral replication, serving as a hot target for drug design. GC376 is able to effectively inhibit the activity of M ^pro, which is due to nucleophilic addition of GC376 by binding covalently with Cys145 in M ^pro active site. Here, we used fluorescence resonance energy transfer (FRET) assay to analyze the IC ₅₀ values of GC376 against M ^pros from six different coronaviruses (SARS-CoV-2, HCoV-229E, HCoV-HUK1, MERS-CoV, SARS-CoV, HCoV-NL63) and five M ^pro mutants (G15S, M49I, K90R, P132H, S46F) from SARS-CoV-2 variants. The results showed that GC376 displays effective inhibition to various coronaviral M ^pros and SARS-CoV-2 M ^pro mutants. In addition, the crystal structures of SARS-CoV-2 M ^pro (wide type)-GC376, SARS-CoV M ^pro-GC376, MERS-CoV M ^pro-GC376, and SARS-CoV-2 M ^pro mutants (G15S, M49I, S46F, K90R, and P132H)-GC376 complexes were solved. We found that GC376 is able to fit into the active site of M ^pros from different coronaviruses and different SARS-CoV-2 variants properly. Detailed structural analysis revealed key molecular determinants necessary for inhibition and illustrated the binding patterns of GC376 to these different M ^pros. In conclusion, we not only proved the inhibitory activity of GC376 against different M ^pros including SARS-CoV-2 M ^pro mutants, but also revealed the molecular mechanism of inhibition by GC376, which will provide scientific guidance for the development of broad-spectrum drugs against SARS-CoV-2 as well as other coronaviruses.

Organizational Affiliation

College of Pharmacy, Gannan Medical University, Ganzhou 341000, China.

Macromolecule Content

Total Structure Weight: 67.86 kDa
Atom Count: 4,733
Modelled Residue Count: 602
Deposited Residue Count: 606
Unique protein chains: 1

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	303	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% 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
UED (Subject of Investigation/LOI) Query on UED 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~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide C₂₁ H₃₁ N₃ O₅ JUCVXDDMQHPCKT-BZSNNMDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B]