Research workbench
Discovery of M5049: a novel selective TLR7/8 inhibitor for treatment of autoimmunity
Analyse Discovery of M5049: a novel selective TLR7/8 inhibitor for treatment of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZJZ
- Type
- protein
- Length
- 1,477 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 8
- UniProt
- Q9NR97
- Ligands
- QLH, NAG, MAN, BMA
- Pockets
- 15 · best druggability 0.78
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 | 737 | 11% helix, 17% strand | Q9NR97 |
| B | Toll-like receptor 8 | protein | 740 | 12% helix, 16% strand | Q9NR97 |
Ligands and binding sites
- QLH · 5-[(3~{R},5~{S})-3-azanyl-5-(trifluoromethyl)piperidin-1-yl]quinoline-8-carbonitrile · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B
- FMT · Formic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.78 | 0.84 | 78 | QLH |
| 2 | 417 | 0.63 | 0.77 | 61 | empty |
| 3 | 234 | 0.59 | 0.80 | 29 | NAG |
| 4 | 214 | 0.58 | 0.80 | 30 | NAG |
| 5 | 165 | 0.54 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1714 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 13 disulfide (N-glycosylation, disulfide).
Compared structures
- 6ZJZ · Discovery of M5049: a novel selective TLR7/8 inhibitor for treatment of autoimmunity · 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 6ZJZ · PDBe 6ZJZ · UniProt Q9NR97
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