MolNFT v1 · #191399 · protein
IRAK4 in complex with compound #3
8DKS · Interleukin-1 receptor-associated kinase 4: “IRAK4 in complex with compound #3”. X-ray diffraction, 1 ligand (SO9), 4 pockets (best druggability 0.82). MolNFT v1 #191399 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 8DKS
- Type
- protein
- Length
- 561 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
- SO9
- Pockets
- 4 · best druggability 0.82
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 | 283 | 41% helix, 17% strand | Q9NWZ3 |
| B | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 278 | 42% helix, 17% strand | Q9NWZ3 |
Ligands and binding sites
- SO9 · (1S,2S,3R,4R)-3-({2-[3-(pyrrolidine-1-carbonyl) anilino]thieno[3,2-d]pyrimidin-4-yl}amino) bicyclo[2.2.1]hept-5-ene-2-carboxamide · ligand · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.82 | 0.83 | 102 | SO9, BME |
| 2 | 287 | 0.67 | 0.82 | 38 | SO9 |
| 3 | 103 | 0.64 | 0.89 | 30 | empty |
| 4 | 63 | 0.59 | 0.90 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 555 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (additive adduct, phosphorylation).
Compared structures
- 8DKS · IRAK4 in complex with compound #3 · 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 8DKS · PDBe 8DKS · UniProt Q9NWZ3
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