MolNFT v2 · #222692 · protein
Crystal structure of IRAK4 kinase domain with compound 9
8V2F · Interleukin-1 receptor-associated kinase 4: “Crystal structure of IRAK4 kinase domain with compound 9”. X-ray diffraction at 2.09, 2 ligands (YJU, CL), 20 pockets (best druggability 0.75). MolNFT v2 #222692 on GenesisL1: 3D…
- PDB
- 8V2F
- Type
- protein
- Length
- 1,191 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.09
- Source
- Homo sapiens
- Molecule
- Interleukin-1 receptor-associated kinase 4
- EC
- 2.7.11.1
- UniProt
- Q9NWZ3
- Ligands
- YJU, CL
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.09 · 4 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 297 | 41% helix, 18% strand | Q9NWZ3 |
| B | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 298 | 41% helix, 18% strand | Q9NWZ3 |
| C | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 302 | 41% helix, 18% strand | Q9NWZ3 |
| D | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 294 | 41% helix, 18% strand | Q9NWZ3 |
Ligands and binding sites
- YJU · N-{2-[(1r,4r)-4-(hydroxymethyl)cyclohexyl]-6-(2-hydroxypropan-2-yl)-2H-indazol-5-yl}-6-(trifluoromethyl)pyridine-2-carboxamide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.75 | 0.84 | 49 | YJU |
| 2 | 699 | 0.73 | 0.79 | 49 | CL |
| 3 | 460 | 0.73 | 0.82 | 54 | YJU, GOL |
| 4 | 514 | 0.71 | 0.80 | 66 | YJU |
| 5 | 410 | 0.71 | 0.82 | 47 | YJU |
Interfaces
4 interfaces between chains.
- A–C · 998 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 973 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 672 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 262 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (phosphorylation).
Compared structures
- Q9NWZ3 · AlphaFold monomer V2.0 prediction for interleukin-1 receptor- associated kinase 4 (Q9NWZ3) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 8V2F · PDBe 8V2F · UniProt Q9NWZ3
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