MolNFT v1 · #70436 · protein
Inhibitors of hepatitis C virus polymerase: synthesis and characterization of novel 6-fluoro-N-[2-hydroxy-1(S)-benzamides
3LKH · RNA-directed RNA polymerase: “Inhibitors of hepatitis C virus polymerase: synthesis and characterization of novel…”. X-ray diffraction, 1 ligand (LT6), 20 pockets (best druggability 0.81). MolNFT v1 #70436 on GenesisL1: 3D…
- PDB
- 3LKH
- Type
- protein
- Length
- 1,112 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
- O92972
- Ligands
- LT6
- Pockets
- 20 · best druggability 0.81
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 | 554 | 49% helix, 16% strand | O92972 |
| B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 558 | 48% helix, 15% strand | O92972 |
Ligands and binding sites
- LT6 · 2-(2-{[(1S)-1-benzyl-2-hydroxyethyl]amino}-2-oxoethoxy)-N-butyl-6-fluoro-N-methylbenzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.81 | 0.95 | 26 | LT6 |
| 2 | 220 | 0.81 | 0.94 | 24 | LT6 |
| 3 | 965 | 0.79 | 0.81 | 85 | empty |
| 4 | 928 | 0.79 | 0.81 | 78 | empty |
| 5 | 170 | 0.58 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 988 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3LKH · Inhibitors of Hepatitis C Virus Polymerase: Synthesis and Characterization of Novel… · 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 3LKH · PDBe 3LKH · UniProt O92972
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