Research workbench
Discovery of lysine-targeted EIF4E inhibitors through covalent docking
Analyse Discovery of lysine-targeted EIF4E inhibitors through covalent docking in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U06
- Type
- protein
- Length
- 728 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 4E
- UniProt
- P63073
- Ligands
- EI8
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Eukaryotic translation initiation factor 4E | protein | 182 | 35% helix, 30% strand | P63073 |
| C | Eukaryotic translation initiation factor 4E | protein | 182 | 28% helix, 31% strand | P63073 |
| D | Eukaryotic translation initiation factor 4E | protein | 182 | 32% helix, 31% strand | P63073 |
Ligands and binding sites
- EI8 · 3-{[(4-cyanophenyl)methyl](1-oxo-1,2-dihydroisoquinolin-7-yl)sulfamoyl}benzene-1-sulfonyl fluoride · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.54 | 0.81 | 20 | EI8 |
| 2 | 190 | 0.54 | 0.79 | 23 | empty |
| 3 | 189 | 0.52 | 0.78 | 21 | EI8 |
| 4 | 159 | 0.49 | 0.77 | 19 | EI8 |
| 5 | 129 | 0.49 | 0.79 | 22 | EI8 |
Interfaces
3 interfaces between chains.
- A–C · 501 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 473 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 433 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6U06 · Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking · the same entry in another collection · chain A against A, TM-score 1.00
- P63073 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E (P63073) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P63073
- Elsewhere: RCSB PDB 6U06 · PDBe 6U06 · UniProt P63073
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