MolNFT v1 · #180080 · protein

The crystal structure of papain-like protease of SARS cov-2 in complex with PLP_SNYDER496 inhibitor

7KOL: “The crystal structure of papain-like protease of SARS cov-2 in complex with PLP_SNYDER496 inhibitor”. X-ray diffraction, 3 ligands (Y96, ZN, CL), 2 pockets (best druggability 0.39). MolNFT v1 #180080 on GenesisL1: 3D structure…

PDB: 7KOL
Type: protein
Length: 308 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Papain-like protease
EC: 3.4.22.-
UniProt: P0DTC1
Ligands: Y96, ZN, CL
Pockets: 2 · best druggability 0.39

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Papain-like protease (EC 3.4.22.-)	protein	308	26% helix, 33% strand	P0DTC1

Ligands and binding sites

Y96 · 5-[(E)-(hydroxyimino)methyl]-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide · ligand · chains A
ZN · Zinc ion · metal · 4 copies · chains A
CL · Chloride ion · ion · 4 copies · chains A
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A

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

Pockets

2 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	76	0.39	0.78	17	Y96
2	94	0.37	0.75	25	empty

Compared structures

7KOL · The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder496… · the same entry in another collection · chain A against A, TM-score 1.00

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 7KOL · PDBe 7KOL · UniProt P0DTC1

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