Research workbench
IRAK4 in complex with inhibitor
Analyse IRAK4 in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LXY
- Type
- protein
- Length
- 1,172 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-1 receptor-associated kinase 4
- EC
- 2.7.11.1
- UniProt
- Q9NWZ3
- Ligands
- EXF, SO4
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 294 | 41% helix, 18% strand | Q9NWZ3 |
| B | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 297 | 40% helix, 18% strand | Q9NWZ3 |
| D | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 293 | 40% helix, 17% strand | Q9NWZ3 |
| E | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 288 | 42% helix, 17% strand | Q9NWZ3 |
Ligands and binding sites
- EXF · N-[(2R)-2-fluoranyl-3-methyl-3-oxidanyl-butyl]-6-[(6-fluoranylpyrazolo[1,5-a]pyrimidin-5-yl)amino]-4-(propan-2-ylamino)pyridine-3-carboxamide · ligand · 4 copies · chains A, B, D, E
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.81 | 0.90 | 65 | empty |
| 2 | 259 | 0.78 | 0.91 | 43 | empty |
| 3 | 176 | 0.75 | 0.91 | 30 | EXF |
| 4 | 199 | 0.74 | 0.90 | 33 | EXF |
| 5 | 729 | 0.74 | 0.79 | 53 | empty |
Interfaces
5 interfaces between chains.
- B–D · 650 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 626 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 536 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 496 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 407 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (phosphorylation).
Compared structures
- 6LXY · IRAK4 in complex with inhibitor · 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 Q9NWZ3
- Elsewhere: RCSB PDB 6LXY · PDBe 6LXY · UniProt Q9NWZ3
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