8QM9: Eukaryotic translation initiation factor 4E

Name: PDB 8QM9: Potential drug binding sites for translation initiation factor eIF4E
Published: 2025-01-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Potential drug binding sites for translation initiation factor eIF4E. Determined by X-ray diffraction at 1.97 Å resolution. Released 15 Jan 2025.

Method: X-ray diffraction
Resolution: 1.97 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,709
Mol. weight: 51.49 kDa
Ligands: W4K
Released: 15 Jan 2025

Explore 8QM9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8QM9 contains 20 α-helices and 16 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	17-22	6
α-helix	31-33	3
β-strand	38-48	11	1
α-helix	56-59	4
β-strand	60-68	9	1
α-helix	69-82	14
β-strand	90-95	6	1
β-strand	111-116	6	1
α-helix	121	1
α-helix	122-126	5
α-helix	127-138	12
α-helix	143-148	6
β-strand	149-155	7	1
β-strand	162-167	6	1
α-helix	173-187	15
β-strand	196-199	4	1
α-helix	200-204	5
β-strand	215-216	2	1

Chain B: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	17-22	6
β-strand	38-49	12	2
α-helix	56-59	4
β-strand	61-68	8	2
α-helix	69-82	14
β-strand	89-95	7	2
β-strand	111-116	6	2
α-helix	117-118	2
α-helix	119-121	3
α-helix	122-126	5
α-helix	127-138	12
α-helix	143-148	6
β-strand	149-155	7	2
β-strand	162-167	6	2
α-helix	173-186	14
β-strand	196-199	4	2
α-helix	200-204	5
β-strand	215-216	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic translation initiation factor 4E	A, B	protein	215	Homo sapiens	P06730 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8QM9_1 Eukaryotic translation initiation factor 4E (chains A, B)
MHHHHHHGARIIYDRAFLMACRGGGGENLYFQGKHPLQNRWALWFFKNDKSKTWQANLRL
ISKFDTVEDFWALYNHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQR
RSDLNRFWLETLLCLIGESFDDYSDDVCGAVVNVRAKGDKIAIWTTECENREAVTHIGRV
YKERLGLPPKIVIGYQSHADTATKSGSTTKNRFVV

Ligands and cofactors

ID	Name	Formula	Copies
W4K	(2~{R})-2-[(1~{S})-1-[4-(2-fluorophenyl)-2-(2-hydroxyethylamino)phenyl]propoxy]…	C20 H26 F N O3	2

Water and common crystallization additives (DMS, PEG, EDO) are not listed.

Primary citation

Integrating fragment-based screening with targeted protein degradation and genetic rescue to explore eIF4E function. Sharp, S.Y., Martella, M., D'Agostino, S. et al. Nat Commun (2024) 15:10037-10037. DOI 10.1038/s41467-024-54356-1 · PubMed

Other PDB entries of the same protein (UniProt P06730 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4TPW 1.5 Å, The co-complex structure of the translation initiation factor eIF4E with the inhibitor…
5T46 1.53 Å, Crystal structure of the human eIF4E-eIF4G complex
8QM8 1.58 Å, Potential drug binding sites for translation initiation factor eIF4E
4TQB 1.59 Å, The co-complex structure of the translation initiation factor eIF4E with the inhibitor…
5ZJY 1.59 Å, Stapled-peptides tailored against initiation of translation
7D6Y 1.67 Å, eIF4E in Complex with a Disulphide-Free Autonomous VH Domain
5ZJZ 1.67 Å, Stapled-peptides tailored against initiation of translation
5EI3 1.71 Å, Co-crystal structure of eIF4E with nucleotide mimetic inhibitor.
4UED 1.75 Å, Complex of human eIF4E with the 4E binding protein 4E-BP1
5ZK9 1.76 Å, Stapled-peptides tailored against initiation of translation
4TQC 1.8 Å, The co-complex structure of the translation initiation factor eIF4E with the inhibitor…
5ZML 1.8 Å, Stapled-peptides tailored against initiation of translation

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