MolNFT v1 · #110783 · protein
Crystal structure of IRAK4 kinase domain with inhibitor
4Y73 · Interleukin-1 receptor-associated kinase 4: “Crystal structure of IRAK4 kinase domain with inhibitor”. X-ray diffraction, 1 ligand (XPY), 13 pockets (best druggability 0.83). MolNFT v1 #110783 on GenesisL1: 3D structure, binding…
- PDB
- 4Y73
- Type
- protein
- Length
- 1,168 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
- XPY
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 292 | 42% helix, 17% strand | Q9NWZ3 |
| B | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 292 | 41% helix, 16% strand | Q9NWZ3 |
| C | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 293 | 42% helix, 18% strand | Q9NWZ3 |
| D | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 291 | 42% helix, 18% strand | Q9NWZ3 |
Ligands and binding sites
- XPY · 5-{[(1R,2S)-2-aminocyclohexyl]amino}-N-[1-methyl-3-(trifluoromethyl)-1H-pyrazol-4-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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.83 | 0.90 | 76 | XPY |
| 2 | 275 | 0.80 | 0.91 | 42 | empty |
| 3 | 301 | 0.80 | 0.90 | 41 | empty |
| 4 | 281 | 0.75 | 0.88 | 45 | XPY |
| 5 | 841 | 0.74 | 0.78 | 62 | empty |
Interfaces
5 interfaces between chains.
- A–D · 695 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 643 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 598 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 540 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 471 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (phosphorylation).
Compared structures
- 4Y73 · Crystal structure of IRAK4 kinase domain with inhibitor · the same entry in another collection · chain B against B, TM-score 1.00
- 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 4Y73 · PDBe 4Y73 · UniProt Q9NWZ3
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