7LTJ

Room-temperature X-ray structure of SARS-CoV-2 main protease (3CL Mpro) in complex with a non-covalent inhibitor Mcule-5948770040


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor.

Clyde, A.Galanie, S.Kneller, D.W.Ma, H.Babuji, Y.Blaiszik, B.Brace, A.Brettin, T.Chard, K.Chard, R.Coates, L.Foster, I.Hauner, D.Kertesz, V.Kumar, N.Lee, H.Li, Z.Merzky, A.Schmidt, J.G.Tan, L.Titov, M.Trifan, A.Turilli, M.Van Dam, H.Chennubhotla, S.C.Jha, S.Kovalevsky, A.Ramanathan, A.Head, M.S.Stevens, R.

(2022) J Chem Inf Model 62: 116-128

  • DOI: 10.1021/acs.jcim.1c00851
  • Primary Citation of Related Structures:  
    7LTJ

  • PubMed Abstract: 
  • Despite the recent availability of vaccines against the acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the search for inhibitory therapeutic agents has assumed importance especially in the context of emerging new viral variants. In this paper, we describe the discovery of a novel noncovalent small-molecule inhibitor, MCULE-5948770040, that binds to and inhibits the SARS-Cov-2 main protease (M pro ) by employing a scalable high-throughput virtual screening (HTVS) framework and a targeted compound library of over 6 ...

    Despite the recent availability of vaccines against the acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the search for inhibitory therapeutic agents has assumed importance especially in the context of emerging new viral variants. In this paper, we describe the discovery of a novel noncovalent small-molecule inhibitor, MCULE-5948770040, that binds to and inhibits the SARS-Cov-2 main protease (M pro ) by employing a scalable high-throughput virtual screening (HTVS) framework and a targeted compound library of over 6.5 million molecules that could be readily ordered and purchased. Our HTVS framework leverages the U.S. supercomputing infrastructure achieving nearly 91% resource utilization and nearly 126 million docking calculations per hour. Downstream biochemical assays validate this M pro inhibitor with an inhibition constant ( K i ) of 2.9 μM (95% CI 2.2, 4.0). Furthermore, using room-temperature X-ray crystallography, we show that MCULE-5948770040 binds to a cleft in the primary binding site of M pro forming stable hydrogen bond and hydrophobic interactions. We then used multiple μs-time scale molecular dynamics (MD) simulations and machine learning (ML) techniques to elucidate how the bound ligand alters the conformational states accessed by M pro , involving motions both proximal and distal to the binding site. Together, our results demonstrate how MCULE-5948770040 inhibits M pro and offers a springboard for further therapeutic design.


    Organizational Affiliation

    National Virtual Biotechnology Laboratory, Washington, District of Columbia 20585, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinaseA306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YD1 (Subject of Investigation/LOI)
Query on YD1

Download Ideal Coordinates CCD File 
B [auth A]6-[4-(3,4-dichlorophenyl)piperazin-1-yl]carbonyl-1~{H}-pyrimidine-2,4-dione
C15 H14 Cl2 N4 O3
XREZIAMDGRLMGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.231α = 90
b = 81.466β = 96.56
c = 88.808γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2021-12-01
    Changes: Database references
  • Version 1.2: 2022-01-19
    Changes: Database references