SMTL ID : 8qm4.1

Potential drug binding sites for translation initiation factor eIF4E

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 5 residues within 4Å: Chain A: W.100, R.110, W.164, H.198, T.201 No protein-ligand interaction detected (PLIP) DMS.5: 4 residues within 4Å: Chain B: F.45, I.61, I.77, M.84 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:F.45

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 5 residues within 4Å: Chain A: K.93, I.96, K.104, D.145, V.147 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.93, A:K.93 PGE.3: 11 residues within 4Å: Chain A: R.59 Chain B: K.93, D.94, G.95, I.96, K.104, D.145, D.146, V.147, C.148, T.166 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.166, B:T.166, A:R.59

2 x W5B: 3-phenylphenol(Non-covalent)

W5B.4: 13 residues within 4Å: Chain A: L.43, F.64, F.70, L.73, Y.74, I.77, Q.78, L.79, S.80, Y.89, L.91, W.128, L.132 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.43, A:L.43, A:F.64, A:F.70, A:L.73, A:Y.74, A:I.77, A:L.91, A:L.132 Hydrogen bonds: A:Q.78 Water bridges: A:S.80 pi-Stacking: A:Y.89, A:W.128 W5B.6: 13 residues within 4Å: Chain B: L.43, F.64, F.70, L.73, Y.74, I.77, Q.78, N.82, L.83, Y.89, L.91, W.128, L.132 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.43, B:L.43, B:F.64, B:F.70, B:L.73, B:I.77, B:N.82, B:L.83, B:Y.89, B:L.91, B:L.132 Hydrogen bonds: B:N.82 pi-Stacking: B:W.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharp, Y.S. et al., Integrating fragment-based screening with targeted protein degradation and genetic rescue to explore eIF4E function. Nat Commun (2025)

Release Date

2025-01-15

Peptides

Eukaryotic translation initiation factor 4E: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Eukaryotic translation initiation factor 4E

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