Research workbench
Structure of the IRAK4 kinase domain with compound 5
Analyse Structure of the IRAK4 kinase domain with compound 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O9D
- Type
- protein
- Length
- 1,137 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.51
- Source
- Homo sapiens
- Molecule
- Interleukin-1 receptor-associated kinase 4
- EC
- 2.7.11.1
- UniProt
- Q9NWZ3
- Ligands
- LTY
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · resolution 2.51 · 4 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 286 | 40% helix, 17% strand | Q9NWZ3 |
| B | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 284 | 40% helix, 18% strand | Q9NWZ3 |
| C | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 283 | 41% helix, 17% strand | Q9NWZ3 |
| D | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 284 | 41% helix, 18% strand | Q9NWZ3 |
Ligands and binding sites
- LTY · N-{7-[4-(aminomethyl)piperidin-1-yl]quinolin-6-yl}pyrazolo[1,5-a]pyrimidine-3-carboxamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.69 | 0.80 | 43 | LTY |
| 2 | 65 | 0.68 | 0.95 | 18 | empty |
| 3 | 756 | 0.68 | 0.75 | 48 | empty |
| 4 | 292 | 0.68 | 0.83 | 42 | LTY |
| 5 | 373 | 0.67 | 0.80 | 41 | LTY |
Interfaces
4 interfaces between chains.
- B–C · 1023 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 892 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 656 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (phosphorylation).
Compared structures
- 6O9D · Structure of the IRAK4 kinase domain with compound 5 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9NWZ3 · AlphaFold monomer V2.0 prediction for interleukin-1 receptor- associated kinase 4 (Q9NWZ3) · a predicted model of the same protein · chain D 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 Q9NWZ3
- Elsewhere: RCSB PDB 6O9D · PDBe 6O9D · UniProt Q9NWZ3
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