6U06: Eukaryotic translation initiation factor 4E

Name: PDB 6U06: Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking
Published: 2019-10-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking. Determined by X-ray diffraction at 1.96 Å resolution. Released 16 Oct 2019.

Method: X-ray diffraction
Resolution: 1.96 Å
Organism: Mus musculus
Chains: 4
Atoms: 6,229
Mol. weight: 90.57 kDa
Ligands: EI8
Released: 16 Oct 2019

Explore 6U06 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6U06 contains 39 α-helices and 36 β-strands across 4 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: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	31-34	4
β-strand	38-49	12	1
α-helix	57-59	3
β-strand	60-68	9	1
α-helix	69-78	10
β-strand	79	1	2
α-helix	82-84	3
α-helix	86	1
β-strand	89-95	7	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	173-186	14
β-strand	196-199	4	1
α-helix	200-204	5
β-strand	215-216	2	1

Chain B: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	31-33	3
β-strand	38-49	12	3
α-helix	56-59	4
β-strand	60-68	9	3
α-helix	69-76	8
β-strand	79	1	4
α-helix	82-84	3
α-helix	86	1
β-strand	89-95	7	3
β-strand	111-116	6	3
α-helix	121	1
α-helix	122-126	5
α-helix	127-138	12
α-helix	143-148	6
β-strand	149-156	8	3
β-strand	162-167	6	3
α-helix	173-186	14
β-strand	196-199	4	3
α-helix	200-204	5
β-strand	215-216	2	3

Chain C: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	2
β-strand	38-49	12	5
β-strand	60-68	9	5
α-helix	69-78	10
α-helix	80-81	2
α-helix	82-84	3
α-helix	86	1
β-strand	89-95	7	5
β-strand	111-117	7	5
α-helix	121-124	4
α-helix	126-138	13
α-helix	143-148	6
β-strand	149-156	8	5
β-strand	161-167	7	5
α-helix	173-187	15
β-strand	196-199	4	5
β-strand	215-216	2	5

Chain D: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	4
β-strand	38-49	12	6
α-helix	57-59	3
β-strand	61-68	8	6
α-helix	69-78	10
α-helix	82-84	3
α-helix	86	1
β-strand	89-95	7	6
β-strand	111-117	7	6
α-helix	121-124	4
α-helix	126-138	13
α-helix	143-148	6
β-strand	149-156	8	6
β-strand	161-167	7	6
α-helix	173-186	14
β-strand	196-199	4	6
α-helix	200-205	6
β-strand	215-216	2	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic translation initiation factor 4E	A, B, C, D	protein	190	Mus musculus	P63073 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6U06_1 Eukaryotic translation initiation factor 4E (chains A, B, C, D)
VANPEHYIKHPLQNRWALWFFKNDKSKTWQANLRLISKFDTVEDFWALYNHIQLSSNLMP
GCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDYSD
DVCGAVVNVRAKGDKIAIWTTECENRDAVTHIGRVYKERLGLPPKIVIGYQSHADTATKS
GSTTKNRFVV

Ligands and cofactors

ID	Name	Formula	Copies
EI8	3-{[(4-cyanophenyl)methyl](1-oxo-1,2-dihydroisoquinolin-7-yl)sulfamoyl}benzene-…	C23 H16 F N3 O5 S2	4

Primary citation

Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking. Wan, X., Yang, T., Cuesta, A. et al. J Am Chem Soc (2020) 142:4960-4964. DOI 10.1021/jacs.9b10377 · PubMed

Other PDB entries of the same protein (UniProt P63073 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5M7X 1.68 Å, Translation initiation factor 4E in complex with (RP)-m2(7,2'O)GppSepG mRNA 5' cap…
5M7Z 1.69 Å, Translation initiation factor 4E in complex with (SP)-m2(7,2'O)GppSepG mRNA 5' cap…
5M7V 1.74 Å, Translation initiation factor 4E in complex with (RP)-m2(7,2'O)GppSpG mRNA 5' cap analog…
5J5Y 1.75 Å, Translation initiation factor 4E in complex with m2(7,2'O)GppCCl2ppG mRNA 5' cap analog
6U09 1.79 Å, Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking
1L8B 1.8 Å, Cocrystal Structure of the Messenger RNA 5' Cap-binding Protein (eIF4E) bound to…
5M84 1.85 Å, Translation initiation factor 4E in complex with (SP)-m2(7,2'O)GppSpA mRNA 5' cap analog
6GKK 1.86 Å, Translation initiation factor 4E in complex with beta-phosphorothioate trinucleotide…
5M83 1.86 Å, Translation initiation factor 4E in complex with (RP)-m2(7,2'O)GppSpA mRNA 5' cap analog
5J5O 1.87 Å, Translation initiation factor 4E in complex with m7GppppG mRNA 5' cap analog
5M81 1.9 Å, Translation initiation factor 4E in complex with (SP)-iPr-m7GppSpG mRNA 5' cap analog
5OSX 1.92 Å, Translation initiation factor 4E in complex with m7G(5'S)ppp(5'S)G mRNA 5' cap analog

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