MolNFT v1 · #165592 · protein
Discovery of lysine-targeted EIF4E inhibitors through covalent docking
6U09 · Eukaryotic translation initiation factor 4E: “Discovery of lysine-targeted EIF4E inhibitors through covalent docking”. X-ray diffraction, 1 ligand (EI9), 5 pockets (best druggability 0.57). MolNFT v1 #165592 on GenesisL1: 3D…
- PDB
- 6U09
- Type
- protein
- Length
- 730 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 4E
- UniProt
- P63073
- Ligands
- EI9
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 4E | protein | 182 | 32% helix, 29% strand | P63073 |
| B | Eukaryotic translation initiation factor 4E | protein | 181 | 33% helix, 29% strand | P63073 |
| C | Eukaryotic translation initiation factor 4E | protein | 184 | 34% helix, 28% strand | P63073 |
| D | Eukaryotic translation initiation factor 4E | protein | 183 | 33% helix, 30% strand | P63073 |
Ligands and binding sites
- EI9 · 3-{(1-oxo-1,2-dihydroisoquinolin-7-yl)[(pyridin-4-yl) methyl]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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.57 | 0.80 | 24 | empty |
| 2 | 106 | 0.50 | 0.81 | 19 | EI9 |
| 3 | 142 | 0.49 | 0.78 | 21 | EI9 |
| 4 | 126 | 0.47 | 0.78 | 20 | EI9 |
| 5 | 161 | 0.47 | 0.76 | 22 | EI9 |
Interfaces
3 interfaces between chains.
- A–D · 444 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 443 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 431 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6U09 · Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking · the same entry in another collection · chain D against D, 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 B 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 6U09 · PDBe 6U09 · UniProt P63073
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