7Q5F | pdb_00007q5f

Crystal structure of F2F-2020216-01X bound to the main protease (3CLpro/Mpro) of SARS-CoV-2.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 
    0.196 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Easy access to alpha-ketoamides as SARS-CoV-2 and MERS M pro inhibitors via the PADAM oxidation route.

Pelliccia, S.Cerchia, C.Esposito, F.Cannalire, R.Corona, A.Costanzi, E.Kuzikov, M.Gribbon, P.Zaliani, A.Brindisi, M.Storici, P.Tramontano, E.Summa, V.

(2022) Eur J Med Chem 244: 114853-114853

  • DOI: https://doi.org/10.1016/j.ejmech.2022.114853
  • Primary Citation Related Structures: 
    7Q5E, 7Q5F

  • PubMed Abstract: 

    SARS-CoV-2 caused worldwide the current outbreak called COVID-19. Despite multiple countermeasures implemented, there is an urgent global need for new potent and efficient antiviral drugs against this pathogen. In this context, the main protease (M pro ) of SARS-CoV-2 is an essential viral enzyme and plays a pivotal role in viral replication and transcription. Its specific cleavage of polypeptides after a glutamine residue has been considered as a key element to design novel antiviral drugs. Herein, we reported the design, synthesis and structure-activity relationships of novel α-ketoamides as covalent reversible inhibitors of M pro , exploiting the PADAM oxidation route. The reported compounds showed μM to nM activities in enzymatic and in the antiviral cell-based assays against SARS-CoV-2 M pro . In order to assess inhibitors' binding mode, two co-crystal structures of SARS-CoV-2 M pro in complex with our inhibitors were solved, which confirmed the covalent binding of the keto amide moiety to the catalytic Cys145 residue of M pro . Finally, in order to interrogate potential broad-spectrum properties, we assessed a selection of compounds against MERS M pro where they showed nM inhibitory potency, thus highlighting their potential as broad-spectrum coronavirus inhibitors.


  • Organizational Affiliation
    • Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy. Electronic address: sveva.pelliccia@unina.it.

Macromolecule Content 

  • Total Structure Weight: 69.33 kDa 
  • Atom Count: 5,407 
  • Modeled Residue Count: 611 
  • Deposited Residue Count: 612 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B
306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
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 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
90X
(Subject of Investigation/LOI)

Query on 90X



Download:Ideal Coordinates CCD File
C [auth A],
H [auth B]
(S)-1-(2-(2,4-dichlorophenoxy)acetyl)-N-((S)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)-4-(phenethylamino)butan-2-yl)pyrrolidine-2-carboxamide
C29 H34 Cl2 N4 O6
GYPKOWHKPVSQIO-RZOLNQLPSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3

Query on NO3



Download:Ideal Coordinates CCD File
I [auth B],
K [auth B]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
L [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free:  0.196 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.866α = 90
b = 100.441β = 90
c = 103.631γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionEuropean Union101003551

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary