Research workbench
IRAK4 in complex with compound 1
Analyse IRAK4 in complex with compound 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K75
- Type
- protein
- Length
- 1,115 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
- 6QX, SO4
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 273 | 41% helix, 16% strand | Q9NWZ3 |
| B | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 276 | 41% helix, 16% strand | Q9NWZ3 |
| C | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 284 | 43% helix, 17% strand | Q9NWZ3 |
| D | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 282 | 43% helix, 17% strand | Q9NWZ3 |
Ligands and binding sites
- 6QX · ~{N}1-(7,8-dihydro-6~{H}-cyclopenta[2,3]thieno[2,4-~{c}]pyrimidin-1-yl)-~{N}4,~{N}4-dimethyl-cyclohexane-1,4-diamine · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.82 | 0.90 | 66 | empty |
| 2 | 325 | 0.81 | 0.91 | 42 | empty |
| 3 | 810 | 0.73 | 0.78 | 51 | empty |
| 4 | 223 | 0.71 | 0.87 | 35 | 6QX |
| 5 | 231 | 0.71 | 0.87 | 36 | 6QX |
Interfaces
5 interfaces between chains.
- A–D · 676 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 618 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 564 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 562 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 438 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (phosphorylation).
Compared structures
- 5K75 · IRAK4 in complex with Compound 1 · 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 5K75 · PDBe 5K75 · UniProt Q9NWZ3
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