MolNFT v1 · #157335 · protein
HCV NS5B 1B N316 bound to compound 18
6MVP · Genome polyprotein: “HCV NS5B 1B N316 bound to compound 18”. X-ray diffraction, 1 ligand (K4S), 15 pockets (best druggability 0.81). MolNFT v1 #157335 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6MVP
- Type
- protein
- Length
- 1,098 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
- P26663
- Ligands
- K4S
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein (EC 3.4.22.-, 3.4.21.98, 3.6.1.15, 3.6.4.13, 2.7.7.48) | protein | 548 | 49% helix, 16% strand | P26663 |
| B | Genome polyprotein (EC 3.4.22.-, 3.4.21.98, 3.6.1.15, 3.6.4.13, 2.7.7.48) | protein | 550 | 49% helix, 16% strand | P26663 |
Ligands and binding sites
- K4S · (4-{[5-cyclopropyl-2-(4-fluorophenyl)-3-(methylcarbamoyl)-1-benzofuran-6-yl](methylsulfonyl) amino}phenyl)boronic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.81 | 0.82 | 98 | K4S |
| 2 | 1054 | 0.81 | 0.82 | 88 | K4S |
| 3 | 1024 | 0.75 | 0.78 | 60 | empty |
| 4 | 103 | 0.50 | 0.81 | 17 | empty |
| 5 | 100 | 0.46 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 453 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6MVP · HCV NS5B 1b N316 bound to Compound 18 · 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 6MVP · PDBe 6MVP · UniProt P26663
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