8IFS

SARS-CoV-2 3CL protease (3CLpro) in complex with compound 7

• PDB DOI: https://doi.org/10.2210/pdb8IFS/pdb

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


• Deposited: 2023-02-19 Released: 2023-10-18 
• Deposition Author(s): Su, H.X., Zhao, W.F., Xie, H., Nie, T.Q., Li, M.J., Xu, Y.C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.295 
• R-Value Work: 0.266 
• R-Value Observed: 0.268 

Literature

Discovery of oral simnotrelvir, an approved SARS-CoV-2 3C-like protease inhibitor for the treatment of COVID-19

Jiang, X., Su, H.

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: 68.76 kDa 
• Atom Count: 4,537 
• 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 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
OZL (Subject of Investigation/LOI)	C [auth A], D [auth B]	(8~{S})-7-[(2~{S})-2-(~{tert}-butylcarbamoylamino)-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-1-cyano-2-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]ethyl]-1,4-dithia-7-azaspiro[4.4]nonane-8-carboxamide C25 H40 N6 O4 S2 BLRKRWSWARPDLL-XLAORIBOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.295 
• R-Value Work: 0.266 
• R-Value Observed: 0.268 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.542	α = 90
b = 82.106	β = 96.91
c = 86.394	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-18 
Deposition Author(s): Su, H.X., Zhao, W.F., Xie, H., Nie, T.Q., Li, M.J., Xu, Y.C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-10-18
  Type: Initial release