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

Experimental Data Snapshot

  • Resolution: 1.25 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1038/s41467-021-20900-6
  • Primary Citation of Related Structures:  

  • 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 ). 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 Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Tokyo, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B
307Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V7G (Subject of Investigation/LOI)
Query on V7G

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C30 H35 N5 O5 S
Query on 1PE

Download Ideal Coordinates CCD File 
C10 H22 O6
Experimental Data & Validation

Experimental Data

  • 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
PDB_EXTRACTdata extraction
xia2data reduction
DIALSdata scaling
Cootmodel building

Structure Validation

View Full Validation Report

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
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description