Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 69.16 kDa 
• Atom Count: 5313 
• Modelled Residue Count: 603 
• Deposited Residue Count: 614 
• Unique protein chains: 1

7JKV

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

• PDB DOI: 10.2210/pdb7JKV/pdb

• Classification: VIRAL PROTEIN/INHIBITOR
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-29 Released: 2020-09-23 
• Deposition Author(s): Bulut, H., Hattori, S.I., Das, D., Murayama, K., Mitsuya, H.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

---

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 

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

• PubMed: 33510133 
• 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 ). 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. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	307	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V7G (Subject of Investigation/LOI)	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
1PE	E [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N

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 = 55.245	α = 90
b = 99.143	β = 107.86
c = 58.903	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
DIALS	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-07-29 
• Released Date: 2020-09-23 
Deposition Author(s): Bulut, H., Hattori, S.I., Das, D., Murayama, K., Mitsuya, H.

---

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

Revision History  

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