ISDA

Deposition Date 2021-02-01

Release Date 2021-06-23

Last Version Date 2023-11-29

Entry Detail

PDB ID:

7E18

Keywords:

HYDROLASE

Title:

Crystal structure of SAR-CoV-2 3CL protease complex with inhibitor YH-53

Biological Source:

Source Organism:

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

Host Organism:

Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.65 Å

R-Value Free:

0.19

R-Value Work:

0.18

R-Value Observed:

0.18

Space Group:

C 1 2 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Replicase polyprotein 1ab
Gene (Uniprot):rep
Chain IDs:A
Chain Length:306
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTD1 Pfam ID:PF05409 EC:2.7.7.48

Ligand Molecules

EDO

HUR

Primary Citation

3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents.

Konno, S, Kobayashi, K, Senda, M, Funai, Y, Seki, Y, Tamai, I, Schakel, L, Sakata, K, Pillaiyar, T, Taguchi, A, Taniguchi, A, Gutschow, M, Muller, C.E, Takeuchi, K, Hirohama, M, Kawaguchi, A, Kojima, M, Senda, T, Shirasaka, Y, Kamitani, W, Hayashi, Y.Show

J.Med.Chem. 65 2926 2939 (2022)

PMID: 34313428 DOI: 10.1021/acs.jmedchem.1c00665

Abstact

The novel coronavirus, SARS-CoV-2, has been identified as the causative agent for the current coronavirus disease (COVID-19) pandemic. 3CL protease (3CLpro) plays a pivotal role in the processing of viral polyproteins. We report peptidomimetic compounds with a unique benzothiazolyl ketone as a warhead group, which display potent activity against SARS-CoV-2 3CLpro. The most potent inhibitor YH-53 can strongly block the SARS-CoV-2 replication. X-ray structural analysis revealed that YH-53 establishes multiple hydrogen bond interactions with backbone amino acids and a covalent bond with the active site of 3CLpro. Further results from computational and experimental studies, including an in vitro absorption, distribution, metabolism, and excretion profile, in vivo pharmacokinetics, and metabolic analysis of YH-53 suggest that it has a high potential as a lead candidate to compete with COVID-19.

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Primary Citation of related structures