8WTI | pdb_00008wti

Crystal structure of the SARS-CoV-2 main protease in complex with 20j

• PDB DOI: https://doi.org/10.2210/pdb8WTI/pdb

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


• Deposited: 2023-10-18 Released: 2024-08-28 
• Deposition Author(s): Zeng, R., Zhao, X., Yang, S.Y., Lei, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.201 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Discovery of alpha-Ketoamide inhibitors of SARS-CoV-2 main protease derived from quaternized P1 groups.

Huang, Q., Quan, B., Chen, Y., Zhao, X., Zhou, Y., Huang, C., Qiao, J., Wang, Y., Li, Y., Yang, S., Lei, J., Li, L.

(2024) Bioorg Chem 143: 107001-107001

• PubMed: 38101266 
• DOI: https://doi.org/10.1016/j.bioorg.2023.107001
• Primary Citation Related Structures: 
  8WTI


• PubMed Abstract: 
  

  Although the SARS-CoV-2 pandemic has ended, multiple sporadic cases still exist, posing a request for more antivirals. The main protease (M ^pro ) of SARS-CoV-2, a key enzyme for viral replication, is an attractive target for drug development. Here, we report the discovery of a new potent α-ketoamide-containing M ^pro inhibitor, N-((R)-1-cyclohexyl-2-(((R)-3-methoxy-1-oxo-1-((1-(2-oxo-2-((thiazol-2-ylmethyl)amino)acetyl)cyclobutyl)amino)propan-2-yl)amino)-2-oxoethyl)-4,4-difluorocyclohexane-1-carboxamide (20j). This compound presented promising enzymatic inhibitory activity against SARS-CoV-2 M ^pro with an IC ₅₀ value of 19.0 nM, and an excellent antiviral activity in cell-based assay with an EC ₅₀ value of 138.1 nM. This novel covalent inhibitor may be used as a lead compound for subsequent drug discovery against SARS-CoV-2.

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Organizational Affiliation: 
• Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China.
Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Frontier Medical Center, Tianfu Jincheng Laboratory, Chengdu, Sichuan 610212, China.
Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China. Electronic address: [e-mail].

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 69.3 kDa 
• Atom Count: 5,697 
• Modeled Residue Count: 609 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	306	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X1Z (Subject of Investigation/LOI)	C [auth A], G [auth B]	~{N}-[(1~{R})-1-cyclohexyl-2-[[(2~{R})-3-methoxy-1-oxidanylidene-1-[[1-[(1~{S})-1-oxidanyl-2-oxidanylidene-2-(1,3-thiazol-2-ylmethylamino)ethyl]cyclobutyl]amino]propan-2-yl]amino]-2-oxidanylidene-ethyl]-4,4-bis(fluoranyl)cyclohexane-1-carboxamide C29 H43 F2 N5 O6 S UHHQICGXTSMHIU-YMPZKCBVSA-N
PEG	D [auth A], E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.201 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.57	α = 90
b = 106.37	β = 103.03
c = 54.43	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOLREP	phasing
Aimless	data scaling
xia2	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-08-28 
Deposition Author(s): Zeng, R., Zhao, X., Yang, S.Y., Lei, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	2021YFF0702004

Revision History  

• Version 1.0: 2024-08-28
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary