5SMM | pdb_00005smm

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 Z1633315555 (Mpro-IBM0058)

• PDB DOI: https://doi.org/10.2210/pdb5SMM/pdb
• Deposition Group: G_1002232 (changed state) | Explore  G_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: 1.58 Å
• R-Value Free: 
  0.231 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

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: 34.55 kDa 
• Atom Count: 2,661 
• Modeled 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
O46 (Subject of Investigation/LOI)	E [auth A]	N-[4-(3-fluorophenyl)oxan-4-yl]-2-(3-hydroxyphenyl)acetamide C19 H20 F N O3 UQVBMSYLQWGFOX-UHFFFAOYSA-N
DMS	B [auth A], C [auth A], D [auth A], F [auth A], G [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.231 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.124	α = 90
b = 53.041	β = 102.9
c = 44.382	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	--

Revision History  

• Version 1.0: 2023-04-26
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection
• Version 1.2: 2026-02-18
  Changes: Refinement description, Structure summary