9GF7 | pdb_00009gf7

SARS-CoV2 Main Protease (Mpro) in complex with the covalent inhibitor 28a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.293 (Depositor), 0.292 (DCC) 
  • R-Value Work: 
    0.256 (Depositor), 0.259 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Synthesis and biological investigation of peptidomimetic SARS-CoV-2 main protease inhibitors bearing quinoline-based heterocycles at P 3.

Rossi, S.Deidda, G.Fiaschi, L.Ibba, R.Pieroni, M.Dichiara, M.Carullo, G.Butini, S.Ramunno, A.Brogi, S.Lolicato, M.Arrigoni, C.Cabella, N.Bavagnoli, L.Maga, G.Varasi, I.Biba, C.Vicenti, I.Gemma, S.Crespan, E.Zazzi, M.Campiani, G.

(2025) Arch Pharm (Weinheim) 358: e2400812-e2400812

  • DOI: https://doi.org/10.1002/ardp.202400812
  • Primary Citation of Related Structures:  
    9GF7

  • PubMed Abstract: 

    In the last few years, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been the cause of a worldwide pandemic, highlighting the need for novel antiviral agents. The main protease (M pro ) of SARS-CoV-2 was immediately identified as a crucial enzyme for viral replication and has been validated as a drug target. Here, we present the design and synthesis of peptidomimetic M pro covalent inhibitors characterized by quinoline-based P 3 moieties. Structure-activity relationships (SARs) were also investigated at P 1 and P 2 , as well as for different warheads. The binding modes of the designed inhibitors were assessed using X-ray crystallographic and molecular docking studies. The identified M pro inhibitors were tested for their antiviral activities in cell-based assays, and the results were encouraging. The SAR studies presented here can contribute to the future design of improved inhibitors by addressing some of the current or prospective issues regarding M pro inhibitors currently used in therapy.


  • Organizational Affiliation
    • Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5306Severe 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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IYL (Subject of Investigation/LOI)
Query on A1IYL

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[(2~{S})-4-methyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]pentan-2-yl]quinoline-8-carboxamide
C23 H28 N4 O4
BECRDGNKPCGVAA-LNLFQRSKSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.293 (Depositor), 0.292 (DCC) 
  • R-Value Work:  0.256 (Depositor), 0.259 (DCC) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.914α = 90
b = 53.134β = 101.158
c = 114.429γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Ministry of EducationItalyPGR16HTPSF

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release