8YLS

Structure of SARS-CoV-2 Mpro in complex with its degrader

• PDB DOI: https://doi.org/10.2210/pdb8YLS/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2024-03-06 Released: 2024-09-04 
• Deposition Author(s): Feng, Y., Li, W., Cheng, S.H., Li, X.B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.222 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

The Main Protease Degraders: Potent Broad-Spectrum Agents for Anti-Coronavirus Agents

Cheng, S.H., Feng, Y., Li, W., Li, X.B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 34.26 kDa 
• Atom Count: 2,557 
• Modelled Residue Count: 306 
• 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 P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1  Go to UniProtKB:  P0DTC1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1LYZ (Subject of Investigation/LOI)	B [auth A]	(4-methoxyphenyl)methyl ~{N}-[(2~{S})-4-methyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]pentan-2-yl]carbamate C22 H31 N3 O6 HCIPLFOANXSFSY-LNLFQRSKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.222 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.12	α = 90
b = 80.82	β = 116.5
c = 54.69	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Feng, Y., Li, W., Cheng, S.H., Li, X.B.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release