7E18 | pdb_00007e18

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

• PDB DOI: https://doi.org/10.2210/pdb7E18/pdb

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2021-02-01 Released: 2021-06-23 
• Deposition Author(s): Senda, M., Konno, S., Hayashi, Y., Senda, T.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.199 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

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.

(2022) J Med Chem 65: 2926-2939

• PubMed: 34313428 
• DOI: https://doi.org/10.1021/acs.jmedchem.1c00665
• Primary Citation Related Structures: 
  7E18, 7E19


• PubMed Abstract: 
  

  The novel coronavirus, SARS-CoV-2, has been identified as the causative agent for the current coronavirus disease (COVID-19) pandemic. 3CL protease (3CL ^pro ) 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 3CL ^pro . 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 3CL ^pro . 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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Organizational Affiliation: 
• School of Pharmacy, Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan.
Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801, Japan.
Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan.
Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn 53121, Germany.
School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan.
Pharmaceutical Institute, Pharmaceutical/Medicinal Chemistry, University of Tübingen, Tübingen 72076, Germany.
Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Koto, Tokyo 135-0064, Japan.
Faculty of Medicine, Transborder Medical Research Center, University of Tsukuba, Tsukuba 305-8575, Japan.
Department of Infectious Diseases and Host Defense, Gunma University Graduate School of Medicine, Maebashi 371-8511, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.84 kDa 
• Atom Count: 2,523 
• Modeled Residue Count: 303 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1ab	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HUR (Subject of Investigation/LOI)	B [auth A]	N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide C30 H33 N5 O5 S JBLLRCOZJMVOAE-HSQYWUDLSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.199 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.154	α = 90
b = 82.673	β = 114.045
c = 51.599	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-23 
Deposition Author(s): Senda, M., Konno, S., Hayashi, Y., Senda, T.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101001

Revision History  

• Version 1.0: 2021-06-23
  Type: Initial release
  
• Version 1.1: 2021-08-11
  Changes: Database references
• Version 1.2: 2022-03-09
  Changes: Database references
• Version 1.3: 2023-11-29
  Changes: Data collection, Refinement description