SMTL ID : 8qm7.1

Potential drug binding sites for translation initiation factor eIF4E

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-dimer

Ligands

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

DMS.1: 4 residues within 4Å: Chain A: W.100, W.164, H.198, T.201 No protein-ligand interaction detected (PLIP) DMS.2: 3 residues within 4Å: Chain A: R.15, E.130, R.184 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.130 DMS.5: 6 residues within 4Å: Chain B: W.100, R.110, W.164, H.198, T.201, A.202 1 PLIP interactions: 1 interactions with chain B Water bridges: B:W.100

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

PGE.3: 4 residues within 4Å: Chain A: A.20, G.33, H.35, E.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.35 Water bridges: A:G.26

2 x W5K: (2~{R})-2-[(1~{R})-1-[4-(2-fluorophenyl)-2-(2-hydroxyethylamino)phenyl]propoxy]propan-1-ol(Non-covalent)

W5K.4: 18 residues within 4Å: Chain A: L.43, F.64, F.70, L.73, Y.74, I.77, Q.78, S.81, N.82, L.83, Y.89, L.91, L.124, N.125, W.128, L.132, V.152, V.154 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.43, A:F.70, A:L.73, A:L.73, A:Y.74, A:I.77, A:Y.89, A:L.132, A:V.152 Water bridges: A:N.125 pi-Stacking: A:Y.89, A:W.128 W5K.7: 17 residues within 4Å: Chain B: L.43, F.64, F.70, L.73, Y.74, I.77, Q.78, S.81, N.82, L.83, Y.89, L.91, L.124, N.125, W.128, L.132, V.152 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.43, B:F.70, B:L.73, B:L.73, B:Y.74, B:I.77, B:Y.89, B:L.132 Hydrogen bonds: B:S.81, B:N.125 pi-Stacking: B:Y.89, B:W.128

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 6 residues within 4Å: Chain A: R.59 Chain B: D.94, I.96, K.104, D.145, V.147 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.104, B:D.145

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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