Research workbench

Hepatitis C virus polymerase NS5B (bk) with fragment-based compounds

Analyse Hepatitis C virus polymerase NS5B (bk) with fragment-based compounds in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4IH6
Type: protein
Length: 1,114 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-directed RNA polymerase
EC: 2.7.7.48
UniProt: P26663
Ligands: 1EP
Pockets: 13 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RNA-directed RNA polymerase (EC 2.7.7.48)	protein	557	49% helix, 15% strand	P26663

Ligands and binding sites

1EP · (5S)-3-(4-tert-butylbenzyl)-5-(propan-2-yl)imidazolidine-2,4-dione · ligand · 2 copies · chains A, B

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

Pockets

13 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	1190	0.80	0.82	83	1EP
2	1187	0.80	0.81	85	1EP
3	351	0.53	0.73	36	empty
4	111	0.50	0.81	20	empty
5	85	0.48	0.82	17	empty

Interfaces

1 interface between chains.

A–B · 105 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4IH6 · Hepatitis C Virus polymerase NS5B (BK) with fragment-based compounds · 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 P26663
Elsewhere: RCSB PDB 4IH6 · PDBe 4IH6 · UniProt P26663

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