8HI9 | pdb_00008hi9

SARS-CoV-2 3CL protease (3CLpro) in complex with Robinetin

• PDB DOI: https://doi.org/10.2210/pdb8HI9/pdb

• Classification: VIRAL PROTEIN/INHIBITOR
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-11-19 Released: 2023-10-25 
• Deposition Author(s): Su, H.X., Xie, H., Li, M.J., Xu, Y.C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.247 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

Discovery of Polyphenolic Natural Products as SARS-CoV-2 M pro Inhibitors for COVID-19.

Kruger, N., Kronenberger, T., Xie, H., Rocha, C., Pohlmann, S., Su, H., Xu, Y., Laufer, S.A., Pillaiyar, T.

(2023) Pharmaceuticals (Basel) 16

• PubMed: 37259339 
• DOI: https://doi.org/10.3390/ph16020190
• Primary Citation Related Structures: 
  8HI9


• PubMed Abstract: 
  

  The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has forced the development of direct-acting antiviral drugs due to the coronavirus disease 2019 (COVID-19) pandemic. The main protease of SARS-CoV-2 is a crucial enzyme that breaks down polyproteins synthesized from the viral RNA, making it a validated target for the development of SARS-CoV-2 therapeutics. New chemical phenotypes are frequently discovered in natural goods. In the current study, we used a fluorogenic assay to test a variety of natural products for their ability to inhibit SARS-CoV-2 M ^pro . Several compounds were discovered to inhibit M ^pro at low micromolar concentrations. It was possible to crystallize robinetin together with SARS-CoV-2 M ^pro , and the X-ray structure revealed covalent interaction with the protease's catalytic Cys145 site. Selected potent molecules also exhibited antiviral properties without cytotoxicity. Some of these powerful inhibitors might be utilized as lead compounds for future COVID-19 research.

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Organizational Affiliation: 
• Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research Göttingen, Kellnerweg 4, 37077 Göttingen, Germany.
Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany.
School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China.
Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany.
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.

Biological Assembly 1  

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

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 68.26 kDa 
• Atom Count: 4,601 
• Modeled Residue Count: 600 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LKR (Subject of Investigation/LOI)	C [auth A], D [auth B]	3,7-bis(oxidanyl)-2-[3,4,5-tris(oxidanyl)phenyl]chromen-4-one C15 H10 O7 SOEDEYVDCDYMMH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.247 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.156	α = 90
b = 54.182	β = 100.89
c = 115.416	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-25 
Deposition Author(s): Su, H.X., Xie, H., Li, M.J., Xu, Y.C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-10-25
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Database references
• Version 1.2: 2026-03-04
  Changes: Refinement description, Structure summary