MolNFT v1 · #157732 · protein
IRAK4 bound to benzoxazole compound
6N8G · Interleukin-1 receptor-associated kinase 4: “IRAK4 bound to benzoxazole compound”. X-ray diffraction, 1 ligand (KFD), 11 pockets (best druggability 0.84). MolNFT v1 #157732 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6N8G
- Type
- protein
- Length
- 1,143 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
- KFD
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 288 | 42% helix, 18% strand | Q9NWZ3 |
| B | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 286 | 42% helix, 18% strand | Q9NWZ3 |
| C | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 289 | 43% helix, 18% strand | Q9NWZ3 |
| D | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 280 | 41% helix, 19% strand | Q9NWZ3 |
Ligands and binding sites
- KFD · N-[2-(morpholin-4-yl)-6-(piperidin-1-yl)-1,3-benzoxazol-5-yl]-6-(1H-pyrrolo[2,3-b]pyridin-5-yl) pyridine-2-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
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 743 | 0.84 | 0.87 | 85 | KFD |
| 2 | 1119 | 0.83 | 0.84 | 119 | empty |
| 3 | 812 | 0.73 | 0.78 | 60 | empty |
| 4 | 188 | 0.72 | 0.89 | 25 | KFD |
| 5 | 819 | 0.72 | 0.77 | 53 | empty |
Interfaces
5 interfaces between chains.
- B–C · 642 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 620 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 560 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 541 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 222 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (phosphorylation).
Compared structures
- 6N8G · IRAK4 bound to benzoxazole compound · 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 6N8G · PDBe 6N8G · UniProt Q9NWZ3
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