MolNFT v1 · #80995 · protein

3-heterocyclyl quinolone bound to HCV NS5B

3UDL · HCV NS5B polymerase: “3-heterocyclyl quinolone bound to HCV NS5B”. X-ray diffraction, 1 ligand (KLI), 20 pockets (best druggability 0.79). MolNFT v1 #80995 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3UDL
Type: protein
Length: 2,220 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HCV NS5B polymerase
UniProt: Q99AU2
Ligands: KLI
Pockets: 20 · best druggability 0.79

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	HCV NS5B polymerase	protein	555	49% helix, 15% strand	Q99AU2

Ligands and binding sites

KLI · 3-(5-benzyl-1,2,4-oxadiazol-3-yl)-6-fluoro-1-[2-fluoro-4-(trifluoromethyl)benzyl]-7-(4-methylpiperazin-1-yl)quinolin-4(1H)-one · ligand · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	920	0.79	0.82	81	empty
2	1005	0.79	0.81	82	empty
3	928	0.79	0.81	77	empty
4	904	0.79	0.81	73	empty
5	78	0.52	0.84	14	empty

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3UDL · 3-heterocyclyl quinolone bound to HCV NS5B · 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 Q99AU2
Elsewhere: RCSB PDB 3UDL · PDBe 3UDL · UniProt Q99AU2

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