MolNFT v1 · #46900 · protein
Crystal structure of IRAK4 kinase domain complexed with staurosporine
2OIC · Interleukin-1 receptor-associated kinase 4: “Crystal structure of IRAK4 kinase domain complexed with staurosporine”. X-ray diffraction, 1 ligand (STU), 13 pockets (best druggability 0.87). MolNFT v1 #46900 on GenesisL1: 3D…
- PDB
- 2OIC
- Type
- protein
- Length
- 1,124 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
- STU
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 279 | 40% helix, 16% strand | Q9NWZ3 |
| B | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 278 | 41% helix, 17% strand | Q9NWZ3 |
| C | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 280 | 39% helix, 17% strand | Q9NWZ3 |
| D | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 287 | 39% helix, 17% strand | Q9NWZ3 |
Ligands and binding sites
- STU · Staurosporine · 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 | 1180 | 0.87 | 0.88 | 145 | empty |
| 2 | 748 | 0.74 | 0.79 | 49 | empty |
| 3 | 786 | 0.72 | 0.78 | 55 | empty |
| 4 | 50 | 0.69 | 0.98 | 22 | empty |
| 5 | 160 | 0.69 | 0.88 | 24 | STU |
Interfaces
5 interfaces between chains.
- A–D · 668 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 594 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 554 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 430 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 401 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified (phosphorylation).
Compared structures
- 2OIC · Crystal structure of IRAK4 kinase domain complexed with staurosporine · the same entry in another collection · chain D against D, 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 D against A, TM-score 0.98
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 2OIC · PDBe 2OIC · UniProt Q9NWZ3
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