MolNFT v1 · #115966 · protein
HCV NS5B in complex with ligand IDX17119-5
5CZB: “HCV NS5B in complex with ligand IDX17119-5”. X-ray diffraction, 2 ligands (55W, SO4), 13 pockets (best druggability 0.80). MolNFT v1 #115966 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5CZB
- Type
- protein
- Length
- 1,112 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS5B
- UniProt
- O92972
- Ligands
- 55W, SO4
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NS5B | protein | 555 | 48% helix, 15% strand | O92972 |
| B | NS5B | protein | 557 | 48% helix, 15% strand | O92972 |
Ligands and binding sites
- 55W · 1-[4-(7-amino-5-methylpyrazolo[1,5-a]pyrimidin-2-yl)phenyl]-3-{[(R)-(2,4-dimethylphenyl)(methoxy)phosphoryl]amino}-1H-pyrazole-4-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 13 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.80 | 0.82 | 97 | GOL, SO4 |
| 2 | 1077 | 0.80 | 0.81 | 81 | PEG, SO4 |
| 3 | 592 | 0.70 | 0.78 | 62 | empty |
| 4 | 128 | 0.49 | 0.80 | 19 | empty |
| 5 | 129 | 0.49 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 346 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5CZB · HCV NS5B in complex with ligand IDX17119-5 · 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 5CZB · PDBe 5CZB · UniProt O92972
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