Research workbench
Structure of the IRAK4 kinase domain with compound 17
Analyse Structure of the IRAK4 kinase domain with compound 17 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O94
- Type
- protein
- Length
- 1,156 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
- LRS, CA
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 292 | 42% helix, 18% strand | Q9NWZ3 |
| B | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 293 | 40% helix, 18% strand | Q9NWZ3 |
| C | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 286 | 41% helix, 18% strand | Q9NWZ3 |
| D | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 285 | 43% helix, 18% strand | Q9NWZ3 |
Ligands and binding sites
- LRS · N-{5-[4-(hydroxymethyl)piperidin-1-yl]-1-methyl-2-(morpholin-4-yl)-1H-benzimidazol-6-yl}pyrazolo[1,5-a]pyrimidine-3-carboxamide · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 660 | 0.74 | 0.80 | 51 | empty |
| 2 | 552 | 0.73 | 0.81 | 62 | empty |
| 3 | 58 | 0.72 | 0.98 | 21 | empty |
| 4 | 63 | 0.71 | 0.97 | 22 | empty |
| 5 | 402 | 0.71 | 0.82 | 61 | LRS |
Interfaces
4 interfaces between chains.
- B–D · 972 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 965 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 758 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 33 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (phosphorylation).
Compared structures
- 6O94 · Structure of the IRAK4 kinase domain with compound 17 · 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 6O94 · PDBe 6O94 · UniProt Q9NWZ3
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