MolNFT v1 · #158942 · protein
Structure of the IRAK4 kinase domain with compound 5
6O9D · Interleukin-1 receptor-associated kinase 4: “Structure of the IRAK4 kinase domain with compound 5”. X-ray diffraction, 1 ligand (LTY), 14 pockets (best druggability 0.69). MolNFT v1 #158942 on GenesisL1: 3D structure, binding sites…
- PDB
- 6O9D
- Type
- protein
- Length
- 1,137 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
- LTY
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · 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 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 6O9D · PDBe 6O9D · UniProt Q9NWZ3
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