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Crystal structure of human interleukin-1 receptor associated kinase 4 (irak 4, cid 100300) in complex with compound NCC00371481 (bsi 107591)
Analyse Crystal structure of human interleukin-1 receptor associated kinase 4 (irak 4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MOM
- Type
- protein
- Length
- 1,166 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
- JX4
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 289 | 42% helix, 18% strand | Q9NWZ3 |
| B | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 289 | 43% helix, 18% strand | Q9NWZ3 |
| C | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 292 | 42% helix, 18% strand | Q9NWZ3 |
| D | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 296 | 41% helix, 18% strand | Q9NWZ3 |
Ligands and binding sites
- JX4 · 6-[7-methoxy-6-(1-methyl-1H-pyrazol-4-yl)imidazo[1,2-a]pyridin-3-yl]-N-[(3R)-pyrrolidin-3-yl]pyridin-2-amine · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.84 | 0.85 | 99 | empty |
| 2 | 506 | 0.81 | 0.87 | 60 | empty |
| 3 | 788 | 0.74 | 0.79 | 56 | empty |
| 4 | 792 | 0.73 | 0.78 | 52 | empty |
| 5 | 174 | 0.71 | 0.89 | 23 | JX4 |
Interfaces
5 interfaces between chains.
- C–D · 603 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 593 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 578 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 536 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 237 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 modified (phosphorylation).
Compared structures
- 6MOM · Crystal structure of human Interleukin-1 receptor associated Kinase 4 (IRAK 4, CID… · 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 6MOM · PDBe 6MOM · UniProt Q9NWZ3
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