MolNFT v1 · #90602 · protein
HCV NS5B polymerase inhibitors: tri-substituted acylhydrazines as tertiary amide bioisosteres
4EO6 · RNA-directed RNA polymerase: “HCV NS5B polymerase inhibitors: tri-substituted acylhydrazines as tertiary amide bioisosteres”. X-ray diffraction, 1 ligand (0S2), 12 pockets (best druggability 0.80). MolNFT v1 #90602 on GenesisL1: 3D…
- PDB
- 4EO6
- Type
- protein
- Length
- 1,117 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
- 0S2
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 557 | 49% helix, 15% strand | P26663 |
| B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 560 | 49% helix, 16% strand | P26663 |
Ligands and binding sites
- 0S2 · 5-(3,3-dimethylbut-1-yn-1-yl)-3-{[(trans-4-methylcyclohexyl)carbonyl](propan-2-yl)amino}thiophene-2-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.80 | 0.81 | 86 | empty |
| 2 | 1045 | 0.80 | 0.81 | 77 | empty |
| 3 | 1164 | 0.76 | 0.79 | 68 | empty |
| 4 | 117 | 0.49 | 0.80 | 21 | empty |
| 5 | 108 | 0.48 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 562 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4EO6 · HCV NS5B polymerase inhibitors: Tri-substituted acylhydrazines as tertiary amide… · 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 4EO6 · PDBe 4EO6 · UniProt P26663
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