Research workbench
HCV NS5B GT1B N316Y with cmpd 32
Analyse HCV NS5B GT1B N316Y with cmpd 32 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KB7
- Type
- protein
- Length
- 1,093 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HCV polymerase
- EC
- 2.7.7.48
- UniProt
- P26663
- Ligands
- 690
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HCV polymerase (EC 2.7.7.48) | protein | 545 | 49% helix, 16% strand | P26663 |
| B | HCV polymerase (EC 2.7.7.48) | protein | 548 | 49% helix, 15% strand | P26663 |
Ligands and binding sites
- 690 · 5-cyclopropyl-2-(4-fluorophenyl)-6-[{2-[(3R)-1-hydroxy-1,3-dihydro-2,1-benzoxaborol-3-yl]ethyl}(methylsulfonyl)amino]-N-methyl-1-benzofuran-3-carboxamide · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.81 | 0.82 | 98 | 690 |
| 2 | 996 | 0.81 | 0.82 | 89 | 690 |
| 3 | 1069 | 0.75 | 0.77 | 69 | empty |
| 4 | 111 | 0.48 | 0.80 | 20 | empty |
| 5 | 114 | 0.46 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 444 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4KB7 · HCV NS5B GT1B N316Y with CMPD 32 · 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 4KB7 · PDBe 4KB7 · UniProt P26663
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