ISDA

Deposition Date 2024-11-08

Release Date 2025-08-20

Last Version Date 2025-09-10

Entry Detail

PDB ID:

9KGJ

Keywords:

HYDROLASE/INHIBOTOR

Title:

Discovery of an orally bioavailable reversible covalent SARS-CoV-2 Mpro inhibitor with pan-coronavirus activity

Biological Source:

Source Organism:

Severe acute respiratory syndrome coronavirus 2 (Taxon ID: 2697049)
synthetic construct (Taxon ID: 32630)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.37 Å

R-Value Free:

0.24

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 1 21 1

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:3C-like proteinase nsp5
Gene (Uniprot):rep
Chain IDs:A, B
Chain Length:311
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTD1 Pfam ID:PF05409 EC:2.7.7.48

Polymer Type:polypeptide(L)
Molecule:(S)-3-((S)-3-cyclobutyl-2-((R)-2-cyclopentyl-N-methyl-2-pivalamidoacetamido)propanamido)-N-cyclopropyl-2-oxo-4-((S)-2-oxopiperidin-3-yl)butanamide
Chain IDs:C, D
Chain Length:4
Number of Molecules:2
Biological Source:synthetic construct

Ligand Molecules

A1L7M

Primary Citation

Discovery of an Orally Bioavailable Reversible Covalent SARS-CoV-2 M pro Inhibitor with Pan-Coronavirus Activity.

Tan, Q.W, Vankadara, S, Fong, J.Y, See, Y.Y, Baburajendran, N, Ng, P.S, Xu, W, Yeo, Y.K, Wang, W, Low, C.H, Tan, L.H, Ju Tay, E.G, Wong, Y.X, Huang, C, Sim, S, Ang, S.H, Min Toh, H.H, Mohammad, J, Wang, G, Liu, B, Tan, S.T, Kwek, P.Z, Dawson, M.D, Oh, Q.Y, Koh, X, Joy, J, Lee, M.A, Stunkel, W, Pendharkar, V, Hentze, H, Lim, S.P, Ethirajulu, K, Brian Chia, C.S, Cherian, J.Show

J.Med.Chem. 68 17087 17102 (2025)

PMID: 40773370 DOI: 10.1021/acs.jmedchem.5c00581

Abstact

Resulting in several million deaths globally, the COVID-19 pandemic has highlighted the criticality of antiviral drugs during a viral pandemic. Herein, we describe our efforts toward targeting SARS-CoV-2 Mpro, a key viral protease, which led to the discovery of compound 18, a reversible covalent inhibitor with potent antiviral activity against several clinical variants of SARS-CoV-2. Compound 18 demonstrated dose-dependent efficacy in a mouse-adapted SARS-CoV-2 infection model, with favorable pharmacokinetic profiles in mice, rats, dogs, and monkeys.

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