Structure of PDB 5ei3 Chain A Binding Site BS02

Receptor Information

>5ei3 Chain A (length=191) Species: 9606 (Homo sapiens)

EVANPEHYIKHPLQNRWALWFFKNDKSKTWQANLRLISKFDTVEDFWALY
NHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDL
DRFWLETLLCLIGESFDDYSDDVCGAVVNVRAKGDKIAIWTTECENREAV
THIGRVYKERLGLPPKIVIGYQSHADTATKSGSTTKNRFVV

Ligand information

• Ligand ID: 5O8
• InChI: InChI=1S/C18H19F3N6O6S/c19-18(20,21)34(31,32)23-6-10-12(28)13(29)16(33-10)27-8-26(7-9-4-2-1-3-5-9)11-14(27)24-17(22)25-15(11)30/h1-5,8,10,12-13,16,23,28-29H,6-7H2,(H2-,22,24,25,30)/p+1/t10-,12-,13-,16-/m1/s1
• InChIKey: NMFHLBUCTTXCHX-XNIJJKJLSA-O
• SMILES:
  OpenEye OEToolkits 2.0.4: c1ccc(cc1)C[n+]2cn(c3c2C(=O)NC(=N3)N)[C@H]4[C@@H]([C@@H]([C@H](O4)CNS(=O)(=O)C(F)(F)F)O)O
  OpenEye OEToolkits 2.0.4: c1ccc(cc1)C[n+]2cn(c3c2C(=O)NC(=N3)N)C4C(C(C(O4)CNS(=O)(=O)C(F)(F)F)O)O
  CACTVS 3.385: NC1=Nc2n(c[n+](Cc3ccccc3)c2C(=O)N1)[CH]4O[CH](CN[S](=O)(=O)C(F)(F)F)[CH](O)[CH]4O
  CACTVS 3.385: NC1=Nc2n(c[n+](Cc3ccccc3)c2C(=O)N1)[C@@H]4O[C@H](CN[S](=O)(=O)C(F)(F)F)[C@@H](O)[C@H]4O
• Formula: C18 H20 F3 N6 O6 S
• Name: ~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-6-oxidanylidene-7-(phenylmethyl)-1~{H}-purin-7-ium-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-1,1,1-tris(fluoranyl)methanesulfonamide
• ChEMBL: CHEMBL5282449
• ZINC: ZINC000584904816
• PDB chain: 5ei3 Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ei3 Design of nucleotide-mimetic and non-nucleotide inhibitors of the translation initiation factor eIF4E: Synthesis, structural and functional characterisation.
• Resolution: 1.71 Å
• Binding residue (original residue number in PDB): W56 M101 W102 E103 R112 W166 A204
• Binding residue (residue number reindexed from 1): W30 M75 W76 E77 R86 W140 A178
• Annotation score: 1
• Binding affinity: MOAD: Kd=56.5uM
  PDBbind-CN: -logKd/Ki=4.25,Kd=56.5uM

Gene Ontology

Molecular Function

• GO:0000339 RNA cap binding
• GO:0000340 RNA 7-methylguanosine cap binding
• GO:0003723 RNA binding
• GO:0003743 translation initiation factor activity
• GO:0005515 protein binding
• GO:0019899 enzyme binding
• GO:0031370 eukaryotic initiation factor 4G binding
• GO:0098808 mRNA cap binding
• GO:0140297 DNA-binding transcription factor binding

Biological Process

• GO:0000082 G1/S transition of mitotic cell cycle
• GO:0001662 behavioral fear response
• GO:0006406 mRNA export from nucleus
• GO:0006412 translation
• GO:0006413 translational initiation
• GO:0006417 regulation of translation
• GO:0010507 negative regulation of autophagy
• GO:0017148 negative regulation of translation
• GO:0019827 stem cell population maintenance
• GO:0030182 neuron differentiation
• GO:0045665 negative regulation of neuron differentiation
• GO:0045931 positive regulation of mitotic cell cycle
• GO:0051028 mRNA transport
• GO:0051168 nuclear export
• GO:0071549 cellular response to dexamethasone stimulus
• GO:0099578 regulation of translation at postsynapse, modulating synaptic transmission

Cellular Component

• GO:0000932 P-body
• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0010494 cytoplasmic stress granule
• GO:0016281 eukaryotic translation initiation factor 4F complex
• GO:0016442 RISC complex
• GO:0016604 nuclear body
• GO:0016607 nuclear speck
• GO:0033391 chromatoid body
• GO:0036464 cytoplasmic ribonucleoprotein granule
• GO:0048471 perinuclear region of cytoplasm
• GO:0070062 extracellular exosome
• GO:0098794 postsynapse
• GO:0098978 glutamatergic synapse

External links

• PDB: RCSB:5ei3, PDBe:5ei3, PDBj:5ei3
• PDBsum: 5ei3
• PubMed: 27592390
• UniProt: P06730|IF4E_HUMAN Eukaryotic translation initiation factor 4E (Gene Name=EIF4E)