Research workbench
Crystal structure of HCV NS5B polymerase with a novel monocyclic dihydropyridinone inhibitor
Analyse Crystal structure of HCV NS5B polymerase with a novel monocyclic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GYN
- Type
- protein
- Length
- 1,114 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
- P26663
- Ligands
- B42
- Pockets
- 14 · 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 | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 557 | 49% helix, 15% strand | P26663 |
Ligands and binding sites
- B42 · N-{3-[(5R)-1-cyclopentyl-4-hydroxy-5-methyl-5-(3-methylbutyl)-2-oxo-1,2,5,6-tetrahydropyridin-3-yl]-1,1-dioxido-4H-1,2,4-benzothiadiazin-7-yl}methanesulfonamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.80 | 0.81 | 80 | B42 |
| 2 | 1150 | 0.80 | 0.81 | 93 | B42 |
| 3 | 850 | 0.73 | 0.77 | 79 | empty |
| 4 | 537 | 0.68 | 0.78 | 60 | empty |
| 5 | 108 | 0.49 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 607 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3GYN · Crystal structure of HCV NS5B polymerase with a novel monocyclic dihydropyridi inhibitor · 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 3GYN · PDBe 3GYN · UniProt P26663
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