Co-crystal structure of EIF4E with nucleotide mimetic inhibitor.

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 29% strand (DSSP).

Ligands and binding sites

• 5PQ · 3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-4-oxidanyl-cyclobut-3-ene-1,2-dione · ligand · 2 copies · chains A, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• C–D · 728 Ų buried · 11 hydrogen bonds · protein-protein
• A–B · 689 Ų buried · 10 hydrogen bonds · protein-protein
• A–C · 495 Ų buried · 7 hydrogen bonds · protein-protein
• A–D · 109 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

• 5EKV · Co-crystal structure of eIF4E with nucleotide mimetic inhibitor. · the same entry in another collection · chain D against D, TM-score 1.00
• P06730 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E (P06730) · a predicted model of the same protein · chain C against A, TM-score 0.98
• Q13541 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E-binding… · a predicted model of the same protein · chain B against A, TM-score 0.70

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 P06730
• Every structure of UniProt Q13541
• Elsewhere: RCSB PDB 5EKV · PDBe 5EKV · UniProt P06730 · UniProt Q13541