8FTL

Crystal structure of the SARS-CoV-2 (COVID-19) main protease (Mpro) in complex with inhibitor Jun89-3-C1

• PDB DOI: https://doi.org/10.2210/pdb8FTL/pdb

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


• Deposited: 2023-01-12 Released: 2024-01-17 
• Deposition Author(s): Lewandowski, E.M., Butler, S.G., Hu, Y., Tan, H., Wang, J., Chen, Y.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.259 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 

Starting Model: experimental

Literature

Crystal structure of the SARS-CoV-2 (COVID-19) main protease (Mpro) in complex with inhibitor Jun89-3-C1

Lewandowski, E.M., Butler, S.G., Hu, Y., Tan, H., Wang, J., Chen, 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: gel filtration

Macromolecule Content

• Total Structure Weight: 68.62 kDa 
• Atom Count: 4,880 
• Modelled Residue Count: 608 
• 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  Gene Names: rep, 1a-1b 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
5ZF (Subject of Investigation/LOI)	C [auth A], D [auth B]	N-([1,1'-biphenyl]-4-yl)-2-chloro-N-[(1R)-2-oxo-2-{[(1S)-1-phenylethyl]amino}-1-(pyridin-3-yl)ethyl]acetamide C29 H26 Cl N3 O2 XQECDPKLDAEYEC-RBTNQOKQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.259 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.365	α = 90
b = 53.725	β = 101.38
c = 113.799	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-17 
Deposition Author(s): Lewandowski, E.M., Butler, S.G., Hu, Y., Tan, H., Wang, J., Chen, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI158775

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary