7QBB

Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 18


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses.

Luttens, A.Gullberg, H.Abdurakhmanov, E.Vo, D.D.Akaberi, D.Talibov, V.O.Nekhotiaeva, N.Vangeel, L.De Jonghe, S.Jochmans, D.Krambrich, J.Tas, A.Lundgren, B.Gravenfors, Y.Craig, A.J.Atilaw, Y.Sandstrom, A.Moodie, L.W.K.Lundkvist, A.van Hemert, M.J.Neyts, J.Lennerstrand, J.Kihlberg, J.Sandberg, K.Danielson, U.H.Carlsson, J.

(2022) J Am Chem Soc 144: 2905-2920

  • DOI: https://doi.org/10.1021/jacs.1c08402
  • Primary Citation of Related Structures:  
    7AU4, 7B2J, 7B2U, 7B5Z, 7B77, 7BIJ, 7NBT, 7NEO, 7O46, 7QBB

  • PubMed Abstract: 

    Drugs targeting SARS-CoV-2 could have saved millions of lives during the COVID-19 pandemic, and it is now crucial to develop inhibitors of coronavirus replication in preparation for future outbreaks. We explored two virtual screening strategies to find inhibitors of the SARS-CoV-2 main protease in ultralarge chemical libraries. First, structure-based docking was used to screen a diverse library of 235 million virtual compounds against the active site. One hundred top-ranked compounds were tested in binding and enzymatic assays. Second, a fragment discovered by crystallographic screening was optimized guided by docking of millions of elaborated molecules and experimental testing of 93 compounds. Three inhibitors were identified in the first library screen, and five of the selected fragment elaborations showed inhibitory effects. Crystal structures of target-inhibitor complexes confirmed docking predictions and guided hit-to-lead optimization, resulting in a noncovalent main protease inhibitor with nanomolar affinity, a promising in vitro pharmacokinetic profile, and broad-spectrum antiviral effect in infected cells.


  • Organizational Affiliation

    Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-75124 Uppsala, Sweden.


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 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V1B (Subject of Investigation/LOI)
Query on V1B

Download Ideal Coordinates CCD File 
C [auth A]7-isoquinolin-4-yl-2-phenyl-5,7-diazaspiro[3.4]octane-6,8-dione
C21 H17 N3 O2
BWBPGOKJGLWQEA-NBEIKUQISA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
B [auth A],
D [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.768α = 90
b = 53.821β = 101.46
c = 44.992γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
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: 2022-02-23
    Type: Initial release
  • Version 1.1: 2022-03-02
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description