MolNFT v1 · #78813 · protein
I. novel HCV NS5B polymerase inhibitors: discovery of indole 2- carboxylic acids with C3-heterocycles
3SKE · HCV NS5B RNA_DEPENDENT RNA polymerase: “I. novel HCV NS5B polymerase inhibitors: discovery of indole 2- carboxylic acids with C3-heterocycles”. X-ray diffraction, 2 ligands (054, PO4), 16 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 3SKE
- Type
- protein
- Length
- 1,121 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HCV NS5B RNA_DEPENDENT RNA polymerase
- EC
- 2.7.7.48
- UniProt
- O92972
- Ligands
- 054, PO4
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HCV NS5B RNA_DEPENDENT RNA polymerase (EC 2.7.7.48) | protein | 563 | 48% helix, 15% strand | O92972 |
| B | HCV NS5B RNA_DEPENDENT RNA polymerase (EC 2.7.7.48) | protein | 558 | 48% helix, 15% strand | O92972 |
Ligands and binding sites
- 054 · 1-[(2-aminopyridin-4-yl)methyl]-3-(2,4-dioxo-1,2-dihydrothieno[3,4-d]pyrimidin-3(4H)-yl)-5-(trifluoromethyl)-1H-indole-2-carboxylic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.81 | 0.82 | 78 | 054 |
| 2 | 1084 | 0.80 | 0.81 | 82 | 054 |
| 3 | 157 | 0.51 | 0.79 | 25 | empty |
| 4 | 98 | 0.48 | 0.81 | 19 | empty |
| 5 | 134 | 0.47 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1022 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3SKE · I. Novel HCV NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids with… · 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 3SKE · PDBe 3SKE · UniProt O92972
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