MolNFT v1 · #112713 · protein
IRAK4-inhibitor co-structure
4ZTM · Interleukin-1 receptor-associated kinase 4: “IRAK4-inhibitor co-structure”. X-ray diffraction, 1 ligand (4S2), 17 pockets (best druggability 0.81). MolNFT v1 #112713 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4ZTM
- Type
- protein
- Length
- 1,143 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
- 4S2
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 290 | 40% helix, 17% strand | Q9NWZ3 |
| B | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 283 | 38% helix, 15% strand | Q9NWZ3 |
| C | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 285 | 41% helix, 17% strand | Q9NWZ3 |
| D | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 285 | 41% helix, 16% strand | Q9NWZ3 |
Ligands and binding sites
- 4S2 · 5-(1,3-benzothiazol-2-yl)-2-(cyclopropylamino)-6-{[(1R,2S,3R,4R)-2,3-dihydroxy-4-(hydroxymethyl)cyclopentyl]amino}pyrimidin-4(3H)-one · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.81 | 0.88 | 68 | empty |
| 2 | 313 | 0.79 | 0.90 | 44 | empty |
| 3 | 496 | 0.78 | 0.86 | 69 | empty |
| 4 | 745 | 0.74 | 0.79 | 52 | empty |
| 5 | 786 | 0.71 | 0.77 | 57 | empty |
Interfaces
5 interfaces between chains.
- A–D · 658 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 632 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 625 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 545 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 350 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (phosphorylation).
Compared structures
- 4ZTM · Irak4-inhibitor co-structure · 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 4ZTM · PDBe 4ZTM · UniProt Q9NWZ3
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