Structure of PDB 2w97 Chain A Binding Site BS02

Receptor Information

>2w97 Chain A (length=187) Species: 9606 (Homo sapiens)

PEHYIKHPLQNRWALWFFKNDKSKTWQANLRLISKFDTVEDFWALYNHIQ
LSSNLMPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFW
LETLLCLIGESFDDYSDDVCGAVVNVRAKGDKIAIWTTECENREAVTHIG
RVYKERLGLPPKIVIGYQSHADTATKSGSTTKNRFVV

Ligand information

• Ligand ID: MGO
• InChI: InChI=1S/C12H19N4O14P3/c1-15-4-16(5-2-7(13)14-11(19)8(5)15)12-10(18)9(17)6(28-12)3-27-32(23,24)30-33(25,26)29-31(20,21)22/h2,4,6,9-10,12,17-18H,3H2,1H3,(H6-,13,14,19,20,21,22,23,24,25,26)/p+1/t6-,9-,10-,12-/m1/s1
• InChIKey: LPHBJZOLBGBNJF-XYHAGOFUSA-O
• SMILES:
  OpenEye OEToolkits 1.5.0: C[n+]1cn(c2c1C(=O)NC(=C2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
  CACTVS 3.341: C[n+]1cn([CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O)c3C=C(N)NC(=O)c13
  CACTVS 3.341: C[n+]1cn([C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O)c3C=C(N)NC(=O)c13
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n1c[n+](c2c1C=C(N)NC2=O)C)C(O)C3O
  OpenEye OEToolkits 1.5.0: C[n+]1cn(c2c1C(=O)NC(=C2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)O
• Formula: C12 H20 N4 O14 P3
• Name: [[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE
• ZINC: ZINC000016052587
• PDB chain: 2w97 Chain A Residue 1218

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2w97 Crystallization of eIF4E complexed with eIF4GI peptide and glycerol reveals distinct structural differences around the cap-binding site.
• Resolution: 2.29 Å
• Binding residue (original residue number in PDB): W56 M101 W102 E103 R157 K162 G208
• Binding residue (residue number reindexed from 1): W26 M71 W72 E73 R127 K132 G178
• Annotation score: 1
• Binding affinity: MOAD: Kd~9nM

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:2w97, PDBe:2w97, PDBj:2w97
• PDBsum: 2w97
• PubMed: 19440045
• UniProt: P06730|IF4E_HUMAN Eukaryotic translation initiation factor 4E (Gene Name=EIF4E)