8HTV

SARS-CoV-2 3CL protease (3CLpro) in complex with compound 3a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery and Mechanism Study of SARS-CoV-2 3C-like Protease Inhibitors with a New Reactive Group.

Ren, P.Li, H.Nie, T.Jian, X.Yu, C.Li, J.Su, H.Zhang, X.Li, S.Yang, X.Peng, C.Yin, Y.Zhang, L.Xu, Y.Liu, H.Bai, F.

(2023) J Med Chem 66: 12266-12283

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00818
  • Primary Citation of Related Structures:  
    8HTV

  • PubMed Abstract: 

    3CL pro is an attractive target for the treatment of COVID-19. Using the scaffold hopping strategy, we identified a potent inhibitor of 3CL pro ( 3a ) that contains a thiocyanate moiety as a novel warhead that can form a covalent bond with Cys145 of the protein. Tandem mass spectrometry (MS/MS) and X-ray crystallography confirmed the mechanism of covalent formation between 3a and the protein in its catalytic pocket. Moreover, several analogues of compound 3a were designed and synthesized. Among them, compound 3h shows the best inhibition of 3CL pro with an IC 50 of 0.322 μM and a k inact / K i value of 1669.34 M -1 s -1 , and it exhibits good target selectivity for 3CL pro against host proteases. Compound 3c inhibits SARS-CoV-2 in Vero E6 cells (EC 50 = 2.499 μM) with low cytotoxicity (CC 50 > 200 μM). These studies provide ideas and insights to explore and develop new 3CL pro inhibitors in the future.


  • Organizational Affiliation

    School of Life Science and Technology, and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase306Severe acute respiratory syndrome coronavirus 2Mutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UZF (Subject of Investigation/LOI)
Query on UZF

Download Ideal Coordinates CCD File 
B [auth A]1-(5,6-dihydrobenzo[b][1]benzazepin-11-yl)-2-sulfanyl-ethanone
C16 H15 N O S
LSKXZDXJGRPCMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.265α = 90
b = 53.66β = 101.2
c = 44.642γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Database references