MolNFT v1 · #135186 · protein
Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase in complex with 3-[(4-CHLOROPHENYL)METHOXY]-2-(1-oxo-1,3- dihydro-2H-isoindol-2-YL)BENZOIC acid
5TRI: “Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase in complex with…”. X-ray diffraction, 3 ligands (23E, 7HM, SO4), 18 pockets (best druggability 0.80). MolNFT v1 #135186 on GenesisL1: 3D structure, binding…
- PDB
- 5TRI
- Type
- protein
- Length
- 1,087 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS5B RNA-dependent RNA polymerase
- EC
- 2.7.7.48
- UniProt
- Q9WMX2
- Ligands
- 23E, 7HM, SO4
- Pockets
- 18 · 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 RNA-dependent RNA polymerase (EC 2.7.7.48) | protein | 542 | 49% helix, 15% strand | Q9WMX2 |
| B | NS5B RNA-dependent RNA polymerase (EC 2.7.7.48) | protein | 545 | 48% helix, 15% strand | Q9WMX2 |
Ligands and binding sites
- 23E · (2E)-3-(4-{[(1-{[(13-cyclohexyl-6-oxo-6,7-dihydro-5H-indolo[1,2-d][1,4]benzodiazepin-10-yl)carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-enoic acid · ligand · 2 copies · chains A, B
- 7HM · 3-[(4-chlorophenyl)methoxy]-2-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)benzoic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.80 | 0.81 | 75 | 7HM, SO4 |
| 2 | 941 | 0.79 | 0.81 | 77 | 7HM, SO4 |
| 3 | 100 | 0.48 | 0.81 | 21 | empty |
| 4 | 101 | 0.45 | 0.79 | 16 | empty |
| 5 | 110 | 0.44 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 949 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5TRI · CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE IN COMPLEX… · 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 Q9WMX2
- Elsewhere: RCSB PDB 5TRI · PDBe 5TRI · UniProt Q9WMX2
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