MolNFT v1 · #138090 · protein
Crystal structure of irak-4 with a 4,6-diaminonicotinamide inhibitor (compound number 9)
5W85 · Interleukin-1 receptor-associated kinase 4: “Crystal structure of irak-4 with a 4,6-diaminonicotinamide inhibitor (compound number 9)”. X-ray diffraction, 1 ligand (9YS), 4 pockets (best druggability 0.72). MolNFT v1 #138090 on…
- PDB
- 5W85
- Type
- protein
- Length
- 563 residues
- Chains
- 2
- 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
- 9YS
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 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 | 281 | 42% helix, 17% strand | Q9NWZ3 |
| B | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 282 | 41% helix, 17% strand | Q9NWZ3 |
Ligands and binding sites
- 9YS · 6-[(1,3-benzothiazol-6-yl)amino]-4-{[(2S)-1-hydroxy-3-phenylpropan-2-yl]amino}-N-methylpyridine-3-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.72 | 0.78 | 51 | empty |
| 2 | 432 | 0.70 | 0.81 | 43 | 9YS |
| 3 | 347 | 0.66 | 0.80 | 40 | 9YS |
| 4 | 68 | 0.30 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 666 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (phosphorylation).
Compared structures
- 5W85 · Crystal structure of irak-4 with a 4,6-diaminonicotinamide inhibitor (compound number 9) · 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 5W85 · PDBe 5W85 · UniProt Q9NWZ3
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