5SMN

PanDDA analysis group deposition of SARS-CoV-2 main protease ligands identified from single sequence-guideddeep generative framework -- Crystal structure of SARS-CoV-2 main protease in complex with Z1365651030 (Mpro-IBM0078)

• PDB DOI: https://doi.org/10.2210/pdb5SMN/pdb
• Deposition Group: G_1002232 (changed state) ExploreG_1002232

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


• Deposited: 2022-04-20 Released: 2023-04-26 
• Deposition Author(s): Fearon, D., Owen, C.D., Lukacik, P., Strain-Damerell, C.M., von Delft, F.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.212 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Literature

PanDDA analysis group deposition of SARS-CoV-2 main protease ligands identified from single sequence-guideddeep generative framework

Fearon, D., Owen, C.D., Lukacik, P., Strain-Damerell, C.M., von Delft, F.

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)

Macromolecule Content

• Total Structure Weight: 34.34 kDa 
• Atom Count: 2,656 
• Modelled Residue Count: 304 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O4F (Subject of Investigation/LOI)	E [auth A]	N-(1-cyanocyclopropyl)-1-(3-methylpyridin-4-yl)piperidine-4-carboxamide C16 H20 N4 O VADYKWPOUVEKIU-UHFFFAOYSA-N
DMS	B [auth A], C [auth A], D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.212 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.926	α = 90
b = 52.568	β = 102.93
c = 44.593	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-26 
Deposition Author(s): Fearon, D., Owen, C.D., Lukacik, P., Strain-Damerell, C.M., von Delft, F.

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Funding Organization	Location	Grant Number
Not funded	United Kingdom	None

Revision History  

• Version 1.0: 2023-04-26
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection