SMTL ID : 8qm8.1

Potential drug binding sites for translation initiation factor eIF4E

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 4 residues within 4Å: Chain A: D.14, R.15, E.130, R.184 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.15, A:R.184 Water bridges: A:A.16, A:R.184 PEG.2: 3 residues within 4Å: Chain A: R.22, G.23, N.75 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.75 Water bridges: A:R.22, A:G.23 PEG.3: 3 residues within 4Å: Chain A: A.72, L.73, H.76 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.73 PEG.5: 8 residues within 4Å: Chain A: I.113, T.114, Q.119, F.127, L.187, I.191, V.192, I.193 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.114, A:T.114, A:Q.119 PEG.10: 6 residues within 4Å: Chain B: R.126, E.130, E.183, R.184, L.185, G.186 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:D.94, B:E.183 Hydrogen bonds: B:R.126, B:E.130, B:E.130 PEG.11: 7 residues within 4Å: Chain B: I.113, T.114, Q.119, L.187, I.191, V.192, I.193 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.114, B:Q.119

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

PGE.4: 9 residues within 4Å: Chain A: K.93, D.94, G.95, I.96, K.104, D.145, V.147, C.148, T.166 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.166 Water bridges: A:K.93, A:G.95

2 x W4K: (2~{R})-2-[(1~{S})-1-[4-(2-fluorophenyl)-2-(2-hydroxyethylamino)phenyl]propoxy]propan-1-ol(Non-covalent)

W4K.6: 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, D.125, W.128, L.132, V.152, V.154 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.70, A:L.73, A:L.73, A:Y.74, A:I.77, A:I.77, A:I.77, A:L.83, A:Y.89, A:Y.89, A:Y.89, A:L.124, A:L.132, A:L.132, A:V.152 Hydrogen bonds: A:Y.74, A:D.125 Water bridges: A:Y.74, A:D.125 W4K.12: 18 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, D.125, W.128, L.132, V.152, V.154 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.70, B:L.73, B:L.73, B:Y.74, B:I.77, B:I.77, B:L.83, B:L.83, B:Y.89, B:L.132, B:L.132, B:V.152 Hydrogen bonds: B:D.125 Water bridges: B:D.125 pi-Stacking: B:Y.89, B:W.128

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

DMS.7: 4 residues within 4Å: Chain B: L.29, Y.30, F.31, Q.32 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.32 DMS.8: 3 residues within 4Å: Chain B: F.17, A.20, C.21 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:F.17 DMS.9: 6 residues within 4Å: Chain B: I.96, K.104, D.145, V.147, C.148, T.166 No protein-ligand interaction detected (PLIP)

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