7S4B

Room temperature X-ray structure of SARS-CoV-2 main protease in complex with compound Z1530724963


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor.

Glaser, J.Sedova, A.Galanie, S.Kneller, D.W.Davidson, R.B.Maradzike, E.Del Galdo, S.Labbe, A.Hsu, D.J.Agarwal, R.Bykov, D.Tharrington, A.Parks, J.M.Smith, D.M.A.Daidone, I.Coates, L.Kovalevsky, A.Smith, J.C.

(2022) Acs Pharmacol Transl Sci 5: 255-265

  • DOI: https://doi.org/10.1021/acsptsci.2c00026
  • Primary Citation of Related Structures:  
    7S3K, 7S3S, 7S4B

  • PubMed Abstract: 

    Inhibition of the SARS-CoV-2 main protease (M pro ) is a major focus of drug discovery efforts against COVID-19. Here we report a hit expansion of non-covalent inhibitors of M pro . Starting from a recently discovered scaffold (The COVID Moonshot Consortium. Open Science Discovery of Oral Non-Covalent SARS-CoV-2 Main Protease Inhibitor Therapeutics. bioRxiv 2020.10.29.339317) represented by an isoquinoline series, we searched a database of over a billion compounds using a cheminformatics molecular fingerprinting approach. We identified and tested 48 compounds in enzyme inhibition assays, of which 21 exhibited inhibitory activity above 50% at 20 μM. Among these, four compounds with IC 50 values around 1 μM were found. Interestingly, despite the large search space, the isoquinolone motif was conserved in each of these four strongest binders. Room-temperature X-ray structures of co-crystallized protein-inhibitor complexes were determined up to 1.9 Å resolution for two of these compounds as well as one of the stronger inhibitors in the original isoquinoline series, revealing essential interactions with the binding site and water molecules. Molecular dynamics simulations and quantum chemical calculations further elucidate the binding interactions as well as electrostatic effects on ligand binding. The results help explain the strength of this new non-covalent scaffold for M pro inhibition and inform lead optimization efforts for this series, while demonstrating the effectiveness of a high-throughput computational approach to expanding a pharmacophore library.


  • Organizational Affiliation

    Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States.


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 
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
87H (Subject of Investigation/LOI)
Query on 87H

Download Ideal Coordinates CCD File 
B [auth A](2R)-2-(3-fluorophenyl)-N-(isoquinolin-4-yl)propanamide
C18 H15 F N2 O
YZVOKFXROIBJSM-GFCCVEGCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.373α = 90
b = 54.407β = 101
c = 114.284γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-15
    Type: Initial release
  • Version 1.1: 2022-05-04
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description