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Group deposition SARS-CoV-2 main protease in complex with inhibitors from the COVID Moonshot -- Crystal Structure of SARS-CoV-2 main protease in complex with RAL-MED-2de63afb-14 (Mpro-x10387)

Analyse Group deposition SARS-CoV-2 main protease in complex with inhibitors from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7GBN
Type: protein
Length: 304 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.944
Source: Severe acute respiratory syndrome coronavirus 2
Molecule: 3C-like proteinase
EC: 3.4.22.69
UniProt: P0DTD1
Ligands: KXR
Pockets: 4 · best druggability 0.53

Structure

x-ray diffraction · resolution 1.944 · 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

KXR · N-(3-fluoro-5-{[(2S)-4-oxoazetidin-2-yl]oxy}phenyl)-2-(pyrimidin-5-yl)acetamide · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	220	0.53	0.77	29	KXR
2	99	0.49	0.81	18	DMS
3	51	0.33	0.78	16	empty
4	71	0.31	0.74	15	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 7GBN · PDBe 7GBN · UniProt P0DTD1

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