MolNFT v1 · #37778 · protein
Structure of a proline sulfonamide inhibitor bound to HCV NS5B polymerase
2GC8 · RNA-directed RNA polymerase: “Structure of a proline sulfonamide inhibitor bound to HCV NS5B polymerase”. X-ray diffraction, 1 ligand (885), 13 pockets (best druggability 0.81). MolNFT v1 #37778 on GenesisL1: 3D structure, binding…
- PDB
- 2GC8
- 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
- Q99AU2
- Ligands
- 885
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 557 | 48% helix, 15% strand | Q99AU2 |
| B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 555 | 48% helix, 15% strand | Q99AU2 |
Ligands and binding sites
- 885 · 1-[(2-amino-4-chloro-5-methylphenyl)sulfonyl]-L-proline · ligand · 2 copies · chains A, B
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 | 1099 | 0.81 | 0.82 | 82 | 885 |
| 2 | 1092 | 0.80 | 0.81 | 80 | 885 |
| 3 | 314 | 0.56 | 0.76 | 48 | empty |
| 4 | 99 | 0.50 | 0.82 | 18 | empty |
| 5 | 108 | 0.48 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 214 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2GC8 · Structure of a Proline Sulfonamide Inhibitor Bound to HCV NS5b Polymerase · 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 Q99AU2
- Elsewhere: RCSB PDB 2GC8 · PDBe 2GC8 · UniProt Q99AU2
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