MolNFT v2 · #225844 · protein

Crystal structure of SARS-Cov-2 main protease in complex with X77

8YKJ · Non-structural protein 11: “Crystal structure of SARS-Cov-2 main protease in complex with X77”. X-ray diffraction at 1.99, 1 ligand (X77), 7 pockets (best druggability 0.75). MolNFT v2 #225844 on GenesisL1: 3D structure, binding…

PDB: 8YKJ
Type: protein
Length: 598 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.99
Source: Severe acute respiratory syndrome coronavirus 2
Molecule: Non-structural protein 11
UniProt: P0DTC1
Ligands: X77
Pockets: 7 · best druggability 0.75

Structure

x-ray diffraction · resolution 1.99 · 2 distinct chains · 25% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Non-structural protein 11	protein	297	25% helix, 30% strand	P0DTC1
B	Non-structural protein 11	protein	301	26% helix, 29% strand	P0DTC1

Ligands and binding sites

X77 · N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1095	0.75	0.78	95	empty
2	319	0.66	0.81	53	empty
3	322	0.60	0.77	50	empty
4	228	0.51	0.76	28	X77
5	207	0.49	0.76	28	X77

Interfaces

1 interface between chains.

A–B · 1124 Å² buried · 21 hydrogen bonds · protein-protein

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 P0DTC1
Elsewhere: RCSB PDB 8YKJ · PDBe 8YKJ · UniProt P0DTC1

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