Research workbench
Crystal structure of the unphosphorylated IRAK4 kinase domain bound to a type I inhibitor
Analyse Crystal structure of the unphosphorylated IRAK4 kinase domain bound to a type I… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EGD
- Type
- protein
- Length
- 544 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
- J87
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 276 | 43% helix, 16% strand | Q9NWZ3 |
| A | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 268 | 45% helix, 16% strand | Q9NWZ3 |
Ligands and binding sites
- J87 · N-[2-methoxy-4-(morpholin-4-yl)phenyl]-2-(pyridin-3-yl)-1,3-thiazole-5-carboxamide · ligand · 2 copies · chains D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.69 | 0.83 | 40 | J87 |
| 2 | 340 | 0.67 | 0.81 | 44 | J87 |
| 3 | 119 | 0.51 | 0.81 | 22 | empty |
| 4 | 132 | 0.45 | 0.77 | 18 | empty |
| 5 | 61 | 0.43 | 0.82 | 17 | empty |
Interfaces
1 interface between chains.
- D–A · 766 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6EGD · Crystal structure of the unphosphorylated IRAK4 kinase domain Bound to a type I inhibitor · the same entry in another collection · chain D against D, 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 6EGD · PDBe 6EGD · UniProt Q9NWZ3
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