7NT4

X-ray structure of SCoV2-PLpro in complex with small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Acriflavine, a clinically approved drug, inhibits SARS-CoV-2 and other betacoronaviruses.

Napolitano, V.Dabrowska, A.Schorpp, K.Mourao, A.Barreto-Duran, E.Benedyk, M.Botwina, P.Brandner, S.Bostock, M.Chykunova, Y.Czarna, A.Dubin, G.Frohlich, T.Holscher, M.Jedrysik, M.Matsuda, A.Owczarek, K.Pachota, M.Plettenburg, O.Potempa, J.Rothenaigner, I.Schlauderer, F.Slysz, K.Szczepanski, A.Greve-Isdahl Mohn, K.Blomberg, B.Sattler, M.Hadian, K.Popowicz, G.M.Pyrc, K.

(2022) Cell Chem Biol 29: 774

  • DOI: https://doi.org/10.1016/j.chembiol.2021.11.006
  • Primary Citation of Related Structures:  
    7NT4

  • PubMed Abstract: 

    The COVID-19 pandemic caused by SARS-CoV-2 has been socially and economically devastating. Despite an unprecedented research effort and available vaccines, effective therapeutics are still missing to limit severe disease and mortality. Using high-throughput screening, we identify acriflavine (ACF) as a potent papain-like protease (PL pro ) inhibitor. NMR titrations and a co-crystal structure confirm that acriflavine blocks the PL pro catalytic pocket in an unexpected binding mode. We show that the drug inhibits viral replication at nanomolar concentration in cellular models, in vivo in mice and ex vivo in human airway epithelia, with broad range activity against SARS-CoV-2 and other betacoronaviruses. Considering that acriflavine is an inexpensive drug approved in some countries, it may be immediately tested in clinical trials and play an important role during the current pandemic and future outbreaks.


  • Organizational Affiliation

    Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 3
A, B
318Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
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
PRL (Subject of Investigation/LOI)
Query on PRL

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
M [auth B]
N [auth B]
C [auth A],
D [auth A],
E [auth A],
M [auth B],
N [auth B],
O [auth B]
PROFLAVIN
C13 H11 N3
WDVSHHCDHLJJJR-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
T [auth B],
U [auth B],
V [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
J [auth A],
S [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
P [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
P [auth B],
Q [auth B],
R [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.37α = 90
b = 116.37β = 90
c = 253.566γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary