MolNFT v1 · #96791 · protein
Crystal structure of HCV NS5B polymerase in complex with compound 4
4JTZ · Genome polyprotein: “Crystal structure of HCV NS5B polymerase in complex with compound 4”. X-ray diffraction, 2 ligands (1NW, MG), 13 pockets (best druggability 0.80). MolNFT v1 #96791 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4JTZ
- Type
- protein
- Length
- 1,120 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- EC
- 3.4.22.-, 3.4.21.98, 3.6.1.15, 3.6.4.13, 2.7.7.48
- UniProt
- O92972
- Ligands
- 1NW, MG
- 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 | Genome polyprotein (EC 3.4.22.-, 3.4.21.98, 3.6.1.15, 3.6.4.13, 2.7.7.48) | protein | 560 | 49% helix, 15% strand | O92972 |
Ligands and binding sites
- 1NW · 3-{[4-oxo-1-(2,4,6-trifluorobenzyl)-1,4-dihydroquinazolin-6-yl]oxy}-N-(pyridin-3-yl)-2-(trifluoromethyl)benzamide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1055 | 0.80 | 0.82 | 87 | GOL |
| 2 | 1044 | 0.80 | 0.81 | 80 | GOL, MG |
| 3 | 146 | 0.51 | 0.79 | 18 | empty |
| 4 | 132 | 0.48 | 0.79 | 23 | empty |
| 5 | 141 | 0.45 | 0.76 | 19 | 1NW |
Interfaces
1 interface between chains.
- A–B · 976 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4JTZ · Crystal structure of hcv ns5b polymerase in complex with compound 4 · 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 O92972
- Elsewhere: RCSB PDB 4JTZ · PDBe 4JTZ · UniProt O92972
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