MolNFT v1 · #92892 · protein
Crystal structure of HCV NS5B polymerase in complex with a thumb inhibitor
4GMC: “Crystal structure of HCV NS5B polymerase in complex with a thumb inhibitor”. X-ray diffraction, 2 ligands (1BI, SO4), 15 pockets (best druggability 0.80). MolNFT v1 #92892 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4GMC
- Type
- protein
- Length
- 1,100 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS5B polymerase
- EC
- 2.7.7.48
- UniProt
- O92972
- Ligands
- 1BI, SO4
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NS5B polymerase (EC 2.7.7.48) | protein | 559 | 48% helix, 15% strand | O92972 |
| B | NS5B polymerase (EC 2.7.7.48) | protein | 541 | 47% helix, 14% strand | O92972 |
Ligands and binding sites
- 1BI · 3-cyclohexyl-2-(furan-3-yl)-1-[2-(morpholin-4-yl)-2-oxoethyl]-N-(phenylsulfonyl)-1H-indole-6-carboxamide · ligand · chains B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.80 | 0.82 | 96 | SO4 |
| 2 | 882 | 0.78 | 0.81 | 80 | SO4 |
| 3 | 110 | 0.51 | 0.82 | 19 | empty |
| 4 | 78 | 0.50 | 0.83 | 15 | empty |
| 5 | 115 | 0.48 | 0.80 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1049 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4GMC · Crystal structure of HCV NS5B polymerase in complex with a thumb inhibitor · 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 4GMC · PDBe 4GMC · UniProt O92972
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