MolNFT v1 · #186192 · protein
Crystal structure of human TLR8 in complex with compound 4
7R54 · Toll-like receptor 8: “Crystal structure of human TLR8 in complex with compound 4”. X-ray diffraction, 4 ligands (I5B, NAG, MAN), 14 pockets (best druggability 0.80). MolNFT v1 #186192 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7R54
- 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
- I5B, NAG, MAN, BMA
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 8 | protein | 740 | 10% helix, 16% strand | Q9NR97 |
| B | Toll-like receptor 8 | protein | 734 | 11% helix, 16% strand | Q9NR97 |
Ligands and binding sites
- I5B · (5-methoxy-6-pyridin-4-yl-1~{H}-indazol-3-yl)-(4-methylpiperazin-1-yl)methanone · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, 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
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.80 | 0.95 | 43 | empty |
| 2 | 378 | 0.79 | 0.88 | 37 | empty |
| 3 | 154 | 0.79 | 0.95 | 40 | empty |
| 4 | 805 | 0.75 | 0.79 | 91 | I5B |
| 5 | 54 | 0.63 | 0.93 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1123 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 7R54 · Crystal structure of human TLR8 in complex with Compound 4 · 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 7R54 · PDBe 7R54 · UniProt Q9NR97
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