Research workbench
Discovery of imidazoquinolines as a novel class of potent, selective and in vivo efficacious cot kinase inhibitors
Analyse Discovery of imidazoquinolines as a novel class of potent, selective and in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IU2
- Type
- protein
- Length
- 625 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase kinase kinase 8
- EC
- 2.7.11.25
- UniProt
- P41279
- Ligands
- 6DA
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase kinase kinase 8 (EC 2.7.11.25) | protein | 312 | 33% helix, 19% strand | P41279 |
| B | Mitogen-activated protein kinase kinase kinase 8 (EC 2.7.11.25) | protein | 313 | 33% helix, 19% strand | P41279 |
Ligands and binding sites
- 6DA · N-[2-(morpholin-4-yl)ethyl]-6-(8-phenyl-1H-imidazo[4,5-c][1,7]naphthyridin-1-yl)-1,3-benzothiazol-2-amine · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.72 | 0.84 | 45 | 6DA |
| 2 | 326 | 0.72 | 0.84 | 46 | 6DA |
| 3 | 516 | 0.69 | 0.79 | 65 | empty |
| 4 | 458 | 0.66 | 0.78 | 51 | empty |
Interfaces
1 interface between chains.
- A–B · 1127 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5IU2 · Discovery of imidazoquinolines as a novel class of potent, selective and in vivo… · the same entry in another collection · chain A against A, TM-score 1.00
- P41279 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase kinase kinase 8… · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P41279
- Elsewhere: RCSB PDB 5IU2 · PDBe 5IU2 · UniProt P41279
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