5RL3

PanDDA analysis group deposition of computational designs of SARS-CoV-2 main protease covalent inhibitors -- Crystal Structure of SARS-CoV-2 main protease in complex with LON-WEI-adc59df6-39 (Mpro-x3117)

• PDB DOI: https://doi.org/10.2210/pdb5RL3/pdb
• Deposition Group: G_1002163 (changed state) ExploreG_1002163

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


• Deposited: 2020-08-05 Released: 2020-12-02 
• Deposition Author(s): Fearon, D., Owen, C.D., Douangamath, A., Lukacik, P., Powell, A.J., Strain-Damerell, C.M., Zaidman, D., Krojer, T., Gehrtz, P., Wild, C., Aimon, A., Brandao-Neto, J., Carbery, A., Dunnett, L., Gorrie-Stone, T.J., Skyner, R., London, N., Walsh, M.A., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 0.205 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Literature

PanDDA analysis group deposition of computational designs of SARS-CoV-2 main protease covalent inhibitors

Fearon, D., Owen, C.D., Douangamath, A., Lukacik, P., Powell, A.J., Strain-Damerell, C.M., Zaidman, D., Krojer, T., Gehrtz, P., Wild, C., Aimon, A., Brandao-Neto, J., Carbery, A., Dunnett, L., Gorrie-Stone, T.J., Skyner, R., London, N., Walsh, M.A., 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: 34.56 kDa 
• Atom Count: 2,742 
• 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
VEP (Subject of Investigation/LOI)	F [auth A]	N-(4-tert-butylphenyl)-N-[(1R)-2-[(oxan-4-yl)amino]-2-oxo-1-(pyridin-3-yl)ethyl]propanamide C25 H33 N3 O3 RRENCBKXJJGAMC-HSZRJFAPSA-N
DMS	B [auth A], C [auth A], D [auth A], E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 0.205 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.059	α = 90
b = 52.832	β = 103.02
c = 44.547	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-02 
Deposition Author(s): Fearon, D., Owen, C.D., Douangamath, A., Lukacik, P., Powell, A.J., Strain-Damerell, C.M., Zaidman, D., Krojer, T., Gehrtz, P., Wild, C., Aimon, A., Brandao-Neto, J., Carbery, A., Dunnett, L., Gorrie-Stone, T.J., Skyner, R., London, N., Walsh, M.A., von Delft, F.

Revision History  

• Version 1.0: 2020-12-02
  Type: Initial release
  
• Version 1.1: 2021-07-07
  Changes: Database references, Structure summary
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Structure summary