Research workbench
Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase complex with bms-791325 also known as (1AR,12BS)-8- cyclohexyl-N-(dimethylsulfamoyl)-11-methoxy-1A-{[(1R,5S)-3-methyl-3, 8-DIAZABICYCLO[3.2.1]OCT-8-YL]CARBONYL}-1,1A,2,12B- TETRAHYDROCYCLOPROPA[D]INDOLO[2,1-A][2]BENZAZEPINE-5-carboxamide and 2-(4-fluorophenyl)-N-methyl-6-[(METHYLSULFONYL)AMINO]-5-(propan-2- yloxy)-1-benzofuran-3-carboxamide
Analyse Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NLD
- Type
- protein
- Length
- 500 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase
- EC
- 2.7.7.48
- UniProt
- Q9WMX2
- Ligands
- 2N7, 2N5, SO4
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 500 | 50% helix, 14% strand | Q9WMX2 |
Ligands and binding sites
- 2N7 · (1aR,12bS)-8-cyclohexyl-N-(dimethylsulfamoyl)-11-methoxy-1a-{[(1R,5S)-3-methyl-3,8-diazabicyclo[3.2.1]oct-8-yl]carbonyl}-1,1a,2,12b-tetrahydrocyclopropa[d]indolo[2,1-a][2]benzazepine-5-carboxamide · ligand · chains A
- 2N5 · 2-(4-fluorophenyl)-N-methyl-6-[(methylsulfonyl)amino]-5-(propan-2-yloxy)-1-benzofuran-3-carboxamide · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.72 | 0.77 | 82 | 2N5 |
| 2 | 168 | 0.49 | 0.77 | 20 | SO4 |
| 3 | 60 | 0.45 | 0.83 | 14 | empty |
| 4 | 110 | 0.40 | 0.76 | 26 | empty |
| 5 | 59 | 0.39 | 0.80 | 13 | empty |
Compared structures
- 4NLD · Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase complex with… · 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 4NLD · PDBe 4NLD · UniProt Q9WMX2
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