MolNFT v1 · #125045 · protein
IRAK4-inhibitor co-structure
5KX8 · Interleukin-1 receptor-associated kinase 4: “IRAK4-inhibitor co-structure”. X-ray diffraction, 1 ligand (6YE), 13 pockets (best druggability 0.82). MolNFT v1 #125045 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KX8
- Type
- protein
- Length
- 1,145 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
- 6YE
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 4 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 | 288 | 41% helix, 17% strand | Q9NWZ3 |
| B | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 281 | 39% helix, 16% strand | Q9NWZ3 |
| C | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 290 | 41% helix, 17% strand | Q9NWZ3 |
| D | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 286 | 42% helix, 17% strand | Q9NWZ3 |
Ligands and binding sites
- 6YE · ~{N}-(3-aminocarbonyl-1-methyl-pyrazol-4-yl)-5-piperazin-1-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
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 471 | 0.82 | 0.89 | 62 | empty |
| 2 | 372 | 0.79 | 0.89 | 53 | empty |
| 3 | 788 | 0.74 | 0.79 | 59 | empty |
| 4 | 891 | 0.74 | 0.77 | 70 | empty |
| 5 | 183 | 0.72 | 0.89 | 31 | 6YE |
Interfaces
5 interfaces between chains.
- A–D · 674 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 652 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 621 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 580 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 252 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 modified (phosphorylation).
Compared structures
- 5KX8 · Irak4-inhibitor co-structure · 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 5KX8 · PDBe 5KX8 · UniProt Q9NWZ3
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