8IFR

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

• PDB DOI: https://doi.org/10.2210/pdb8IFR/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: 1.66 Å
• R-Value Free: 0.216 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Structure-based development and preclinical evaluation of the SARS-CoV-2 3C-like protease inhibitor simnotrelvir

Jiang, X., Su, H., Shang, W., Zhou, F., Zhang, Y., Zhao, W., Zhang, Q., Xie, H., Jiang, L., Nie, T., Yang, F., Xiong, M., Huang, X., Li, M., Chen, P., Peng, S., Xiao, G., Jiang, H., Tang, R., Zhang, L., Shen, J., Xu, Y.

(2023) Nat Commun 14: 6463

• DOI: https://doi.org/10.1038/s41467-023-42102-y

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: 34.37 kDa 
• Atom Count: 2,584 
• Modelled Residue Count: 305 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	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
P0O (Subject of Investigation/LOI)	B [auth A]	(1R,2S,5S)-3-[(2S)-2-(tert-butylcarbamoylamino)-3,3-dimethyl-butanoyl]-6,6-dimethyl-N-[(2S)-5-oxidanylidene-1-[(3S)-2-oxidanylidenepyrrolidin-3-yl]hex-3-en-2-yl]-3-azabicyclo[3.1.0]hexane-2-carboxamide C29 H47 N5 O5 BKLMFWOPPAUWNX-NWKMKTNDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.216 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.582	α = 90
b = 63.707	β = 90
c = 105.502	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
  
• Version 1.1: 2024-05-01
  Changes: Database references