7NTQ

Crystal structure of the SARS-CoV-2 Main Protease complexed with N-(pyridin-3-ylmethyl)thioformamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.171 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Novel dithiocarbamates selectively inhibit 3CL protease of SARS-CoV-2 and other coronaviruses.

Brier, L.Hassan, H.Hanoulle, X.Landry, V.Moschidi, D.Desmarets, L.Rouille, Y.Dumont, J.Herledan, A.Warenghem, S.Piveteau, C.Carre, P.Ikherbane, S.Cantrelle, F.X.Dupre, E.Dubuisson, J.Belouzard, S.Leroux, F.Deprez, B.Charton, J.

(2023) Eur J Med Chem 250: 115186-115186

  • DOI: https://doi.org/10.1016/j.ejmech.2023.115186
  • Primary Citation of Related Structures:  
    7NTQ, 8AEB

  • PubMed Abstract: 

    Since end of 2019, the global and unprecedented outbreak caused by the coronavirus SARS-CoV-2 led to dramatic numbers of infections and deaths worldwide. SARS-CoV-2 produces two large viral polyproteins which are cleaved by two cysteine proteases encoded by the virus, the 3CL protease (3CL pro ) and the papain-like protease, to generate non-structural proteins essential for the virus life cycle. Both proteases are recognized as promising drug targets for the development of anti-coronavirus chemotherapy. Aiming at identifying broad spectrum agents for the treatment of COVID-19 but also to fight emergent coronaviruses, we focused on 3CL pro that is well conserved within this viral family. Here we present a high-throughput screening of more than 89,000 small molecules that led to the identification of a new chemotype, potent inhibitor of the SARS-CoV-2 3CL pro . The mechanism of inhibition, the interaction with the protease using NMR and X-Ray, the specificity against host cysteine proteases and promising antiviral properties in cells are reported.


  • Organizational Affiliation

    Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France.


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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
35J (Subject of Investigation/LOI)
Query on 35J

Download Ideal Coordinates CCD File 
B [auth A]N-(pyridin-3-ylmethyl)thioformamide
C7 H8 N2 S
HIZAQBZIUYYGKR-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.92α = 90
b = 52.91β = 102.88
c = 44.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata reduction
Aimlessdata scaling
MOLREPphasing
XDSdata processing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2023-03-15
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description