MolNFT v1 · #148325 · protein
IRAK4 in complex with inhibitor
6F3E · Interleukin-1 receptor-associated kinase 4: “IRAK4 in complex with inhibitor”. X-ray diffraction, 2 ligands (CJQ, SO4), 5 pockets (best druggability 0.73). MolNFT v1 #148325 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6F3E
- Type
- protein
- Length
- 556 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
- CJQ, SO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 41% 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 | 40% helix, 16% strand | Q9NWZ3 |
| B | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 284 | 42% helix, 18% strand | Q9NWZ3 |
Ligands and binding sites
- CJQ · 2-[(3~{R})-12-(4-morpholin-4-ylcyclohexyl)oxy-7-thia-9, 11-diazatricyclo[6.4.0.0^{2,6}]dodeca-1(8),2(6),9,11-tetraen-3-yl]ethanamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
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 | 767 | 0.73 | 0.79 | 50 | empty |
| 2 | 356 | 0.69 | 0.82 | 45 | CJQ |
| 3 | 302 | 0.66 | 0.81 | 38 | CJQ |
| 4 | 55 | 0.34 | 0.78 | 11 | empty |
| 5 | 89 | 0.33 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 674 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 6F3E · IRAK4 IN COMPLEX WITH inhibitor · 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 6F3E · PDBe 6F3E · UniProt Q9NWZ3
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