Research workbench

HCV NS5B 1B N316 bound to compound 18

Analyse HCV NS5B 1B N316 bound to compound 18 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MVK
Type: protein
Length: 1,100 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HCV polymerase
UniProt: Q99AU2
Ligands: K4J
Pockets: 11 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HCV polymerase	protein	550	49% helix, 16% strand	Q99AU2
B	HCV polymerase	protein	550	49% helix, 16% strand	Q99AU2

Ligands and binding sites

K4J · (4-{(4S)-3-[5-cyclopropyl-2-(4-fluorophenyl)-3-(methylcarbamoyl)-1-benzofuran-6-yl]-2-oxo-1,3-oxazolidin-4-yl}-2-fluorophenyl)boronic acid · ligand · 2 copies · chains A, B

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

Pockets

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1060	0.81	0.82	97	K4J
2	1147	0.81	0.82	87	K4J
3	1074	0.74	0.77	69	empty
4	95	0.49	0.82	20	empty
5	102	0.47	0.80	19	empty

Interfaces

1 interface between chains.

A–B · 446 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6MVK · HCV NS5B 1b N316 bound to Compound 18 · the same entry in another collection · chain B against B, 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 Q99AU2
Elsewhere: RCSB PDB 6MVK · PDBe 6MVK · UniProt Q99AU2

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