Research workbench
Structure of mk-3281, a potent non-nucleoside finger-loop inhibitor, in complex with the hepatitis C virus NS5B polymerase
Analyse Structure of mk-3281, a potent non-nucleoside finger-loop inhibitor, in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XWY
- Type
- protein
- Length
- 507 residues
- Chains
- 1
- 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
- IB8, MN
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 507 | 50% helix, 16% strand | P26663 |
Ligands and binding sites
- IB8 · (7R)-14-cyclohexyl-7-{[2-(dimethylamino)ethyl](methyl)amino}-7,8-dihydro-6H-indolo[1,2-e][1,5]benzoxazocine-11-carboxylic acid · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.69 | 0.77 | 56 | MN |
| 2 | 202 | 0.51 | 0.77 | 26 | empty |
| 3 | 94 | 0.44 | 0.79 | 19 | IB8 |
| 4 | 74 | 0.38 | 0.78 | 19 | empty |
| 5 | 62 | 0.34 | 0.77 | 13 | empty |
Compared structures
- 2XWY · Structure of MK-3281, a Potent Non-Nucleoside Finger-Loop Inhibitor, in complex with the… · 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 2XWY · PDBe 2XWY · UniProt P26663
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