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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)

Analyse PanDDA analysis group deposition of SARS-CoV-2 main protease ligands identified… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5SMN
Type: protein
Length: 304 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.36
Source: Severe acute respiratory syndrome coronavirus 2
Molecule: 3C-like proteinase
EC: 3.4.22.69
UniProt: P0DTD1
Ligands: O4F
Pockets: 4 · best druggability 0.48

Structure

x-ray diffraction · resolution 1.36 · 1 distinct chain · 26% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase (EC 3.4.22.69)	protein	304	26% helix, 29% strand	P0DTD1

Ligands and binding sites

O4F · N-(1-cyanocyclopropyl)-1-(3-methylpyridin-4-yl)piperidine-4-carboxamide · ligand · chains A
DMS · Dimethyl sulfoxide · additive · 3 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	192	0.48	0.76	25	O4F
2	88	0.47	0.81	19	DMS
3	58	0.31	0.75	16	empty
4	76	0.31	0.74	16	empty

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P0DTD1
Elsewhere: RCSB PDB 5SMN · PDBe 5SMN · UniProt P0DTD1

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