8HVX

Crystal structure of SARS-Cov-2 main protease Y54C mutant in complex with PF07304814

PDB DOI: https://doi.org/10.2210/pdb8HVX/pdb

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

Deposited: 2022-12-28 Released: 2024-01-17
Deposition Author(s): Zhou, X.L., Zhang, J., Li, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.236
R-Value Work: 0.216
R-Value Observed: 0.217

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

Crystal structures of main protease (M pro ) mutants of SARS-CoV-2 variants bound to PF-07304814.

Jiang, H., Zou, X., Zeng, P., Zeng, X., Zhou, X., Wang, J., Zhang, J., Li, J.

(2023) Mol Biomed 4: 23-23

PubMed: 37532968 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/s43556-023-00134-2
Primary Citation of Related Structures:
8HVU, 8HVV, 8HVW, 8HVX, 8HVY, 8HVZ

PubMed Abstract:
There is an urgent need to develop effective antiviral drugs to prevent the viral infection caused by constantly circulating SARS-CoV-2 as well as its variants. The main protease (M ^pro) of SARS-CoV-2 is a salient enzyme that plays a vital role in viral replication and serves as a fascinating therapeutic target. PF-07304814 is a covalent inhibitor targeting SARS-CoV-2 M ^pro with favorable inhibition potency and drug-like properties, thus making it a promising drug candidate for the treatment of COVID-19. We previously solved the structure of PF-07304814 in complex with SARS-CoV-2 M ^pro. However, the binding modes of PF-07304814 with M ^pros from evolving SARS-CoV-2 variants is under-determined. In the current study, we expressed six M ^pro mutants (G15S, K90R, M49I, S46F, V186F, and Y54C) that have been identified in Omicron variants including the recently emerged XBB.1.16 subvariant and solved the crystal structures of PF-07304814 bound to M ^pro mutants. Structural analysis provided insight into the key molecular determinants responsible for the interaction between PF-07304814 and these mutant M ^pros. Patterns for PF-07304814 to bind with these investigated M ^pro mutants and the wild-type M ^pro are generally similar but with some differences as revealed by detailed structural comparison. Structural insights presented in this study will inform the development of novel drugs against SARS-CoV-2 and the possible conformation changes of M ^pro mutants when bound to an inhibitor.

Organizational Affiliation

School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China.

Macromolecule Content

Total Structure Weight: 67.28 kDa
Atom Count: 4,377
Modelled Residue Count: 571
Deposited Residue Count: 598
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	299	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
80I (Subject of Investigation/LOI) Query on 80I 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]	C [auth A], D [auth B]	[(3~{S})-3-[[(2~{S})-2-[(4-methoxy-1~{H}-indol-2-yl)carbonylamino]-4-methyl-pentanoyl]amino]-2-oxidanylidene-4-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]butyl] dihydrogen phosphate C₂₄ H₃₃ N₄ O₉ P FQKALOFOWPDTED-WBAXXEDZSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]