SMTL ID : 8qm9.1

Potential drug binding sites for translation initiation factor eIF4E

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: I.96, K.104, D.145, D.146, V.147, T.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.146 Water bridges: A:K.93 EDO.5: 3 residues within 4Å: Chain B: D.14, R.15, A.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.15, B:R.15, B:A.16 EDO.6: 3 residues within 4Å: Chain B: T.201, K.204, T.209 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.209

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

PEG.2: 3 residues within 4Å: Chain A: F.17, A.20, C.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.20 PEG.7: 7 residues within 4Å: Chain B: K.93, D.94, I.96, K.104, D.145, V.147, T.166 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.166, B:T.166 Water bridges: B:K.93 PEG.9: 4 residues within 4Å: Chain B: W.100, E.101 Ligands: DMS.8, PEG.10 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.50 PEG.10: 4 residues within 4Å: Chain B: N.153, R.155, K.160 Ligands: PEG.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.160

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

DMS.3: 3 residues within 4Å: Chain A: W.100, W.164, H.198 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.100 DMS.8: 6 residues within 4Å: Chain B: W.100, W.164, H.198, T.201, A.202 Ligands: PEG.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.198

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

W4K.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 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.43, A:F.70, A:L.73, A:L.73, A:Y.74, A:Y.74, A:I.77, A:L.83, A:Y.89, A:L.91, A:L.132, A:V.152, A:V.154 Hydrogen bonds: A:N.125 Water bridges: A:Y.74, A:Q.78, A:L.129 pi-Stacking: A:Y.89, A:W.128 W4K.11: 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, N.125, W.128, L.132, V.152, V.154 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.43, B:L.43, B:F.70, B:L.73, B:L.73, B:Y.74, B:I.77, B:Y.89, B:L.91, B:L.132, B:V.152, B:V.154 Hydrogen bonds: B:N.125 Water bridges: B:L.129 pi-Stacking: B:Y.89, 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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