7XAR

Crystal structure of 3C-like protease from SARS-CoV-2 in complex with covalent inhibitor

PDB DOI: https://doi.org/10.2210/pdb7XAR/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-03-18 Released: 2022-11-09
Deposition Author(s): Caaveiro, J.M.M., Ochi, J., Takahashi, D., Ueda, T., Ojida, A.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.206
R-Value Work: 0.173
R-Value Observed: 0.175

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

Discovery of Chlorofluoroacetamide-Based Covalent Inhibitors for Severe Acute Respiratory Syndrome Coronavirus 2 3CL Protease.

Hirose, Y., Shindo, N., Mori, M., Onitsuka, S., Isogai, H., Hamada, R., Hiramoto, T., Ochi, J., Takahashi, D., Ueda, T., Caaveiro, J.M.M., Yoshida, Y., Ohdo, S., Matsunaga, N., Toba, S., Sasaki, M., Orba, Y., Sawa, H., Sato, A., Kawanishi, E., Ojida, A.

(2022) J Med Chem 65: 13852-13865

PubMed: 36229406 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.2c01081
Primary Citation of Related Structures:
7XAR

PubMed Abstract:
The coronavirus disease 2019 (COVID-19) pandemic has necessitated the development of antiviral agents against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 3C-like protease (3CL ^pro) is a promising target for COVID-19 treatment. Here, we report a new class of covalent inhibitors of 3CL ^pro that possess chlorofluoroacetamide (CFA) as a cysteine-reactive warhead. Based on an aza-peptide scaffold, we synthesized a series of CFA derivatives in enantiopure form and evaluated their biochemical efficiency. The data revealed that 8a ( YH-6 ) with the R configuration at the CFA unit strongly blocks SARS-CoV-2 replication in infected cells, and its potency is comparable to that of nirmatrelvir. X-ray structural analysis showed that YH-6 formed a covalent bond with Cys145 at the catalytic center of 3CL ^pro. The strong antiviral activity and favorable pharmacokinetic properties of YH-6 suggest its potential as a lead compound for the treatment of COVID-19.

Organizational Affiliation

Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka812-8582, Japan.

Macromolecule Content

Total Structure Weight: 68.94 kDa
Atom Count: 5,335
Modelled Residue Count: 612
Deposited Residue Count: 612
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	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BOV (Subject of Investigation/LOI) Query on BOV Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B]	H [auth A], K [auth B]	4-fluoranyl-~{N}-[(2~{S})-1-[2-(2-fluoranylethanoyl)-2-[[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]methyl]hydrazinyl]-4-methyl-1-oxidanylidene-pentan-2-yl]-1~{H}-indole-2-carboxamide C₂₂ H₂₇ F₂ N₅ O₄ MRCDFPNCOHGYQJ-GUYCJALGSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	C [auth A], D [auth A], E [auth A], I [auth B], J [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]