MolNFT v2 · #228883 · protein

SARS-CoV-2 Main Protease complexed with (1R)-N-(3-chlorophenyl)-3-oxo-indane-1-carboxamide

9HBQ · 3C-like proteinase nsp5: “SARS-CoV-2 Main Protease complexed with (1R)-N-(3-chlorophenyl)-3-oxo-indane-1-carboxamide”. X-ray diffraction at 1.795, 1 ligand (A1ITO), 4 pockets (best druggability 0.52). MolNFT v2 #228883 on GenesisL1…

PDB: 9HBQ
Type: protein
Length: 305 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.795
Source: Severe acute respiratory syndrome coronavirus 2
Molecule: 3C-like proteinase nsp5
EC: 3.4.22.69
UniProt: P0DTD1
Ligands: A1ITO
Pockets: 4 · best druggability 0.52

Structure

x-ray diffraction · resolution 1.795 · 1 distinct chain · 25% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase nsp5 (EC 3.4.22.69)	protein	305	25% helix, 29% strand	P0DTD1

Ligands and binding sites

A1ITO · (1~{R})-~{N}-(3-chlorophenyl)-3-oxidanylidene-1,2-dihydroindene-1-carboxamide · ligand · chains A
DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
GOL · Glycerol · additive · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	56	0.52	0.87	16	DMS
2	182	0.50	0.77	28	A1ITO
3	66	0.34	0.76	16	empty
4	89	0.34	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 9HBQ · PDBe 9HBQ · UniProt P0DTD1

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