Research workbench
IRAK4 in complex with compound 28
Analyse IRAK4 in complex with compound 28 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K76
- Type
- protein
- Length
- 555 residues
- Chains
- 2
- 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
- 6R1
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 272 | 42% helix, 17% strand | Q9NWZ3 |
| B | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 283 | 42% helix, 16% strand | Q9NWZ3 |
Ligands and binding sites
- 6R1 · ~{N}-(4-morpholin-4-ylcyclohexyl)-5-(oxan-4-yl)-7~{H}-pyrrolo[2,3-d]pyrimidin-4-amine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 758 | 0.73 | 0.78 | 52 | empty |
| 2 | 395 | 0.67 | 0.80 | 43 | 6R1 |
| 3 | 331 | 0.64 | 0.80 | 28 | 6R1 |
| 4 | 63 | 0.35 | 0.78 | 13 | empty |
| 5 | 56 | 0.29 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 636 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 5K76 · IRAK4 in complex with Compound 28 · 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 5K76 · PDBe 5K76 · UniProt Q9NWZ3
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