MolNFT v1 · #180611 · protein

The crystal structure of SARS-cov-2 main protease in complex with demethylated analog of masitinib

7L5D · 3C-like proteinase: “The crystal structure of SARS-cov-2 main protease in complex with demethylated analog of masitinib”. X-ray diffraction, 1 ligand (XNJ), 2 pockets (best druggability 0.50). MolNFT v1 #180611 on GenesisL1: 3D…

PDB: 7L5D
Type: protein
Length: 301 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3C-like proteinase
EC: 3.4.22.69
UniProt: P0DTD1
Ligands: XNJ
Pockets: 2 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase (EC 3.4.22.69)	protein	301	26% helix, 30% strand	P0DTD1

Ligands and binding sites

XNJ · N-(4-methyl-3-{[4-(pyridin-3-yl)-1,3-thiazol-2-yl]amino}phenyl)-4-[(piperazin-1-yl)methyl]benzamide · ligand · chains A
DMS · Dimethyl sulfoxide · additive · 4 copies · chains A
GOL · Glycerol · additive · 4 copies · 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	217	0.50	0.76	31	XNJ, GOL
2	124	0.38	0.74	22	empty

Compared structures

7L5D · The crystal structure of SARS-CoV-2 Main Protease in complex with demethylated analog of… · 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 P0DTD1
Elsewhere: RCSB PDB 7L5D · PDBe 7L5D · UniProt P0DTD1

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