MolNFT v2 · #216625 · protein
Crystal structure of human TLR8 in complex with compound 34
8PFI · Toll-like receptor 8: “Crystal structure of human TLR8 in complex with compound 34”. X-ray diffraction at 2.785, 4 ligands (YHG, NAG, MAN), 13 pockets (best druggability 0.72). MolNFT v2 #216625 on GenesisL1: 3D structure, binding…
- PDB
- 8PFI
- Type
- protein
- Length
- 1,467 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.785
- Source
- Homo sapiens
- Molecule
- Toll-like receptor 8
- UniProt
- Q9NR97
- Ligands
- YHG, NAG, MAN, BMA
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.785 · 2 distinct chains · 9% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 8 | protein | 733 | 9% helix, 16% strand | Q9NR97 |
| B | Toll-like receptor 8 | protein | 734 | 9% helix, 16% strand | Q9NR97 |
Ligands and binding sites
- YHG · (3~{S})-~{N}-[4-[[5-(1,6-dimethylpyrazolo[3,4-b]pyridin-4-yl)-3-methyl-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-1-yl]methyl]-1-bicyclo[2.2.2]octanyl]morpholine-3-carboxamide · 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
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.72 | 0.79 | 74 | YHG |
| 2 | 223 | 0.63 | 0.82 | 30 | NAG |
| 3 | 302 | 0.60 | 0.78 | 39 | NAG |
| 4 | 224 | 0.55 | 0.78 | 21 | empty |
| 5 | 56 | 0.48 | 0.86 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 540 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 18 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- Q9NR97 · AlphaFold monomer V2.0 prediction for toll-like receptor 8 (Q9NR97) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 8PFI · PDBe 8PFI · UniProt Q9NR97
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