SMTL ID : 8qm6.1

Potential drug binding sites for translation initiation factor eIF4E

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

3 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.2: 6 residues within 4Å: Chain A: I.96, K.104, D.145, V.147, C.148, T.166 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.93 DMS.7: 5 residues within 4Å: Chain B: W.100, R.110, W.164, H.198, T.201 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.198

2 x W2N: (1~{S})-1-[4-(2-fluorophenyl)phenyl]ethanol(Non-covalent)

W2N.3: 15 residues within 4Å: Chain A: L.43, F.64, F.70, L.73, Y.74, I.77, S.81, N.82, L.83, Y.89, L.91, N.125, W.128, L.132 Ligands: W4B.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.43, A:L.43, A:F.70, A:L.73, A:Y.74, A:I.77, A:Y.89, A:Y.89, A:L.91, A:L.132 pi-Stacking: A:Y.89, A:W.128 W2N.9: 14 residues within 4Å: Chain B: L.43, F.64, F.70, L.73, Y.74, I.77, S.81, N.82, L.83, Y.89, L.91, W.128, L.132 Ligands: W4B.8 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.43, B:F.70, B:I.77, B:Y.89, B:Y.89, B:L.91, B:L.132, B:L.132 pi-Stacking: B:Y.89, B:W.128

2 x W4B: (1~{R})-1-[4-(2-fluorophenyl)phenyl]ethanol(Non-covalent)

W4B.4: 14 residues within 4Å: Chain A: L.43, F.64, F.70, L.73, Y.74, I.77, Q.78, L.83, Y.89, L.91, N.125, W.128, L.132 Ligands: W2N.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.64, A:F.70, A:L.73, A:Y.74, A:I.77, A:L.83, A:L.91 pi-Stacking: A:Y.89, A:W.128 W4B.8: 15 residues within 4Å: Chain B: L.43, F.64, F.70, L.73, Y.74, I.77, Q.78, S.81, L.83, Y.89, L.91, N.125, W.128, L.132 Ligands: W2N.9 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:L.73, B:Y.74, B:I.77, B:L.83, B:L.91, B:L.132 pi-Stacking: B:Y.89, B:W.128

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

PEG.5: 6 residues within 4Å: Chain A: L.60, I.61, S.62, K.63 Chain B: N.39, R.40 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.63, A:K.63, B:R.40, B:R.40 Water bridges: A:R.40

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

PGE.6: 9 residues within 4Å: Chain A: R.59 Chain B: K.93, D.94, G.95, I.96, K.104, D.145, V.147, T.166 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.166, B:T.166, A:R.59 Water bridges: B:K.93

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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