8SX4: EIF4e

Name: PDB 8SX4: Crystal Structure of eIF4e in complex with Compound 7n
Published: 2023-06-21
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Crystal Structure of eIF4e in complex with Compound 7n. Determined by X-ray diffraction at 1.99 Å resolution. Released 21 Jun 2023.

Method: X-ray diffraction
Resolution: 1.99 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,211
Mol. weight: 45.49 kDa
Ligands: WXL, M7G
Released: 21 Jun 2023

Explore 8SX4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SX4 contains 19 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: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	38-48	11	1
α-helix	56-59	4
β-strand	60-68	9	1
α-helix	69-80	12
β-strand	90-95	6	1
β-strand	111-116	6	1
α-helix	121-124	4
α-helix	126-138	13
α-helix	143-148	6
β-strand	149-155	7	1
β-strand	162-167	6	1
α-helix	173-186	14
β-strand	196-199	4	1
α-helix	200-204	5
β-strand	215-216	2	1

Chain B: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	38-48	11	2
α-helix	56-59	4
β-strand	60-68	9	2
α-helix	69-78	10
α-helix	80-81	2
α-helix	82-84	3
α-helix	86	1
β-strand	90-95	6	2
β-strand	111-116	6	2
α-helix	121	1
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	173-187	15
β-strand	196-199	4	2
α-helix	200-203	4
α-helix	211-213	3
β-strand	215-216	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic translation initiation factor 4E	A, B	protein	191	Homo sapiens	P06730 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8SX4_1 Eukaryotic translation initiation factor 4E (chains A, B)
MVANPEHYIKHPLQNRWALWFFKNDKSKTWQANLRLISKFDTVEDFWALYNHIQLSSNLM
PGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDYS
DDVCGAVVNVRAKGDKIAIWTTECENREAVTHIGRVYKERLGLPPKIVIGYQSHADTATK
SGSTTKNRFVV

Ligands and cofactors

ID	Name	Formula	Copies
WXL	[(~{Z})-4-[2-azanyl-7-[(5-chloranyl-1~{H}-indol-2-yl)methyl]-6-oxidanylidene-1~…	C18 H19 Cl N6 O4 P	1
M7G	7N-methyl-8-hydroguanosine-5'-diphosphate	C11 H18 N5 O11 P2	1

Primary citation

Design of Cell-Permeable Inhibitors of Eukaryotic Translation Initiation Factor 4E (eIF4E) for Inhibiting Aberrant Cap-Dependent Translation in Cancer. Cardenas, E.L., O'Rourke, R.L., Menon, A. et al. J Med Chem (2023) 66:10734-10745. DOI 10.1021/acs.jmedchem.3c00917 · 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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