MolNFT v1 · #131250 · protein

Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase in complex with 4-fluoro-2-(4-fluorophenyl)-N-methyl-5-(2- methyl-5-{[1-(pyrimidin-2-YL)CYCLOPROPYL]CARBAMOYL}PHENYL)-1- benzofuran-3-carboxamide (bms-929075)

5PZP · RNA-directed RNA polymerase: “Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase in complex with…”. X-ray diffraction, 3 ligands (23E, 8XJ, SO4), 19 pockets (best druggability 0.83). MolNFT v1 #131250 on…

PDB: 5PZP
Type: protein
Length: 1,080 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: Q9WMX2
Ligands: 23E, 8XJ, SO4
Pockets: 19 · best druggability 0.83

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA-directed RNA polymerase (EC 2.7.7.48)	protein	545	48% helix, 17% strand	Q9WMX2
B	RNA-directed RNA polymerase (EC 2.7.7.48)	protein	535	49% helix, 16% strand	Q9WMX2

Ligands and binding sites

23E · (2E)-3-(4-{[(1-{[(13-cyclohexyl-6-oxo-6,7-dihydro-5H-indolo[1,2-d][1,4]benzodiazepin-10-yl)carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-enoic acid · ligand · 2 copies · chains A, B
8XJ · 4-fluoro-2-(4-fluorophenyl)-N-methyl-5-(2-methyl-5-{[1-(pyrimidin-2-yl)cyclopropyl]carbamoyl}phenyl)-1-benzofuran-3-carboxamide · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 8 copies · chains A, B
GOL · Glycerol · additive · 4 copies · chains A, B

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

Pockets

19 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	1145	0.83	0.84	94	8XJ
2	1194	0.83	0.84	110	8XJ
3	110	0.50	0.81	17	empty
4	110	0.45	0.78	21	empty
5	108	0.44	0.78	18	empty

Interfaces

1 interface between chains.

A–B · 955 Å² buried · 13 hydrogen bonds · protein-protein

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 Q9WMX2
Elsewhere: RCSB PDB 5PZP · PDBe 5PZP · UniProt Q9WMX2

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