8GTV

SARS-CoV-2 3CL protease (3CLpro) in complex with compound JZD-07

• PDB DOI: https://doi.org/10.2210/pdb8GTV/pdb

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


• Deposited: 2022-09-08 Released: 2023-09-13 
• Deposition Author(s): Su, H.X., Nie, T.Q., 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: 1.80 Å
• R-Value Free: 0.247 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 

Literature

Development of novel inhibitors against SARS-CoV-2 3CLpro

Xu, Y.C., Zang, Y., Zhou, Y.

To be published.

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: 68.65 kDa 
• Atom Count: 4,675 
• Modelled 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	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
KAE (Subject of Investigation/LOI)	C [auth A], D [auth B]	4-[(2~{S})-4-(3,4-dichlorophenyl)-2-(morpholin-4-ylmethyl)piperazin-1-yl]carbonyl-1~{H}-quinolin-2-one C25 H26 Cl2 N4 O3 LBLGMVCPRZTJIF-SFHVURJKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.247 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.647	α = 90
b = 82.133	β = 96.76
c = 89.123	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-13 
Deposition Author(s): Su, H.X., Nie, T.Q., Xie, H., Li, M.J., Xu, Y.C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-09-13
  Type: Initial release