MolNFT v1 · #99926 · protein
Hepatitis C virus polymerase NS5B genotype 1B (bk) in complex with compound 48 (N-({(3S)-1-[6-tert-butyl-5-methoxy-8-(2-oxo-1,2- dihydropyridin-3-YL)QUINOLIN-3-YL]PYRROLIDIN-3-YL}METHYL) methanesulfonamide)
4MIB · RNA-directed RNA polymerase: “Hepatitis C virus polymerase NS5B genotype 1B (bk) in complex with compound 48…”. X-ray diffraction, 1 ligand (28M), 13 pockets (best druggability 0.80). MolNFT v1 #99926 on GenesisL1: 3D structure…
- PDB
- 4MIB
- 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
- 28M
- Pockets
- 13 · 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
- 28M · N-({(3S)-1-[6-tert-butyl-5-methoxy-8-(2-oxo-1,2-dihydropyridin-3-yl)quinolin-3-yl]pyrrolidin-3-yl}methyl)methanesulfonamide · ligand · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.80 | 0.81 | 86 | 28M |
| 2 | 1095 | 0.80 | 0.81 | 86 | 28M |
| 3 | 547 | 0.67 | 0.77 | 59 | empty |
| 4 | 358 | 0.66 | 0.80 | 64 | empty |
| 5 | 123 | 0.49 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 576 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4MIB · Hepatitis C Virus polymerase NS5B genotype 1b (BK) in complex with Compound 48… · 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 4MIB · PDBe 4MIB · UniProt P26663
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