8Y44 | pdb_00008y44

Crystal structure of SARS-CoV-2 3CL protease (3CLpro) in complex with compound 44


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.262 (Depositor) 
  • R-Value Work: 
    0.218 (Depositor) 
  • R-Value Observed: 
    0.220 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of Novel Nonpeptidic and Noncovalent Small Molecule 3CL pro Inhibitors as anti-SARS-CoV-2 Drug Candidate.

Jiang, Z.Feng, B.Chen, L.Nie, T.Chen, S.Wang, L.Liu, H.Yu, T.Zhang, Y.Zheng, M.Xu, Y.Liu, H.Zang, Y.Su, H.Zhang, L.Li, J.Zhou, Y.

(2024) J Med Chem 67: 12760-12783

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00739
  • Primary Citation of Related Structures:  
    8GTV, 8GTW, 8Y42, 8Y44

  • PubMed Abstract: 

    SARS-CoV-2 has still been threatening global public health with its emerging variants. Our previous work reported lead compound JZD-07 that displayed good 3CL pro inhibitory activity. Here, an in-depth structural optimization for JZD-07 was launched to obtain more desirable drug candidates for the therapy of SARS-CoV-2 infection, in which 54 novel derivatives were designed and synthesized by a structure-based drug design strategy. Among them, 24 compounds show significantly enhanced 3CL pro inhibitory potencies with IC 50 values less than 100 nM, and 11 compounds dose-dependently inhibit the replication of the SARS-CoV-2 delta variant. In particular, compound 49 has the most desirable antiviral activity with EC 50 of 0.272 ± 0.013 μM against the delta variant, which was more than 20 times stronger than JZD-07 . Oral administration of 49 could significantly reduce the lung viral copies of mice, exhibiting a more favorable therapeutic potential. Overall, this investigation presents a promising drug candidate for further development to treat SARS-CoV-2 infection.


  • Organizational Affiliation
    • Lingang Laboratory, Shanghai 200031, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5
A, B
306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
EC: 3.4.22.69
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC1 
Go to UniProtKB:  P0DTC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1D50 (Subject of Investigation/LOI)
Query on A1D50

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
~{N}-[(1~{S},2~{R})-2-[(4-bromanyl-2-morpholin-4-ylcarbonyl-6-nitro-phenyl)amino]cyclohexyl]-2-oxidanylidene-1~{H}-quinoline-4-carboxamide
C27 H28 Br N5 O6
KFFVXVXATZDEKJ-YADHBBJMSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.262 (Depositor) 
  • R-Value Work:  0.218 (Depositor) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.97α = 90
b = 89.44β = 90
c = 103.09γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Database references, Structure summary