7JKV

Crystal Structure of SARS-CoV-2 main protease in complex with an inhibitor GRL-2420


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.145 

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Ligand Structure Quality Assessment 


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Literature

A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication.

Hattori, S.I.Higashi-Kuwata, N.Hayashi, H.Allu, S.R.Raghavaiah, J.Bulut, H.Das, D.Anson, B.J.Lendy, E.K.Takamatsu, Y.Takamune, N.Kishimoto, N.Murayama, K.Hasegawa, K.Li, M.Davis, D.A.Kodama, E.N.Yarchoan, R.Wlodawer, A.Misumi, S.Mesecar, A.D.Ghosh, A.K.Mitsuya, H.

(2021) Nat Commun 12: 668-668

  • DOI: 10.1038/s41467-021-20900-6
  • Primary Citation of Related Structures:  
    7JKV

  • PubMed Abstract: 
  • Except remdesivir, no specific antivirals for SARS-CoV-2 infection are currently available. Here, we characterize two small-molecule-compounds, named GRL-1720 and 5h, containing an indoline and indole moiety, respectively, which target the SARS-CoV-2 main protease (M pro ) ...

    Except remdesivir, no specific antivirals for SARS-CoV-2 infection are currently available. Here, we characterize two small-molecule-compounds, named GRL-1720 and 5h, containing an indoline and indole moiety, respectively, which target the SARS-CoV-2 main protease (M pro ). We use VeroE6 cell-based assays with RNA-qPCR, cytopathic assays, and immunocytochemistry and show both compounds to block the infectivity of SARS-CoV-2 with EC 50 values of 15 ± 4 and 4.2 ± 0.7 μM for GRL-1720 and 5h, respectively. Remdesivir permitted viral breakthrough at high concentrations; however, compound 5h completely blocks SARS-CoV-2 infection in vitro without viral breakthrough or detectable cytotoxicity. Combination of 5h and remdesivir exhibits synergism against SARS-CoV-2. Additional X-ray structural analysis show that 5h forms a covalent bond with M pro and makes polar interactions with multiple active site amino acid residues. The present data suggest that 5h might serve as a lead M pro inhibitor for the development of therapeutics for SARS-CoV-2 infection.


    Organizational Affiliation

    Department of Clinical Sciences, Kumamoto University Hospital, Kumamoto, Japan. hmitsuya@hosp.ncgm.go.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinaseA, B307Severe 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V7G (Subject of Investigation/LOI)
Query on V7G

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
N-[(2S)-1-({(1S,2S)-1-(1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
C30 H35 N5 O5 S
DHQWCSDZTRDSRP-XIBGDNMGSA-N
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
E [auth B]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.145 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.245α = 90
b = 99.143β = 107.86
c = 58.903γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
DIALSdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Data collection, Database references