MolNFT v1 · #186387 · protein
Crystal structure of human TLR8 ectodomain bound to small molecule antagonist 21
7RC9 · Toll-like receptor 8: “Crystal structure of human TLR8 ectodomain bound to small molecule antagonist 21”. X-ray diffraction, 4 ligands (RQY, NAG, MAN), 11 pockets (best druggability 0.79). MolNFT v1 #186387 on GenesisL1: 3D…
- PDB
- 7RC9
- Type
- protein
- Length
- 1,474 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 8
- UniProt
- Q9NR97
- Ligands
- RQY, NAG, MAN, BMA
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Toll-like receptor 8 | protein | 737 | 11% helix, 15% strand | Q9NR97 |
Ligands and binding sites
- RQY · 2-(2,6-dimethylpyridin-4-yl)-5-(piperidin-4-yl)-3-(propan-2-yl)-1H-indole · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains B
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.79 | 0.80 | 111 | RQY |
| 2 | 223 | 0.61 | 0.81 | 29 | NAG |
| 3 | 224 | 0.60 | 0.80 | 31 | NAG |
| 4 | 67 | 0.50 | 0.85 | 19 | empty |
| 5 | 240 | 0.49 | 0.74 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 1319 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 7RC9 · Crystal structure of human TLR8 ectodomain bound to small molecule antagonist 21 · 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 Q9NR97
- Elsewhere: RCSB PDB 7RC9 · PDBe 7RC9 · UniProt Q9NR97
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