Structure of PDB 3m93 Chain A Binding Site BS02

Receptor Information

>3m93 Chain A (length=180) Species: 6253 (Ascaris suum)

MRHPLQCHWALWYLKADRSKDWEDCLKQVAVFDTVEDFWSLYNHIQAASG
LTWGSDYYLFKEGIKPMWEDENNVKGGRWLVVVDKQKRAQLLDHYWLELL
MAIIGEQFEDNGEYICGAVVNVRQKGDKVSLWTRDSLKDDVNLRIGQILK
AKLEIPDTEPIRYEVHTGSMVKPRIVIPSK

Ligand information

• Ligand ID: M7G
• InChI: InChI=1S/C11H17N5O11P2/c1-15-3-16(8-5(15)9(19)14-11(12)13-8)10-7(18)6(17)4(26-10)2-25-29(23,24)27-28(20,21)22/h3-4,6-7,10,17-18H,2H2,1H3,(H5-,12,13,14,19,20,21,22,23,24)/p+1/t4-,6-,7-,10-/m1/s1
• InChIKey: SBASPRRECYVBRF-KQYNXXCUSA-O
• SMILES:
  OpenEye OEToolkits 2.0.7: C[n+]1cn(c2c1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)OCC1OC(n2c[n+](C)c3c2N=C(N)NC3=O)C(O)C1O
  OpenEye OEToolkits 2.0.7: C[n+]1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O
  CACTVS 3.385: C[n+]1cn([CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O)c3N=C(N)NC(=O)c13
  CACTVS 3.385: C[n+]1cn([C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O)c3N=C(N)NC(=O)c13
• Formula: C11 H18 N5 O11 P2
• Name: 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
• DrugBank: DB01960
• ZINC: ZINC000013548083
• PDB chain: 3m93 Chain A Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3m93 Structural basis for nematode eIF4E binding an m2,2,7G-Cap and its implications for translation initiation.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): W69 M114 W115 E116 R170
• Binding residue (residue number reindexed from 1): W22 M67 W68 E69 R123
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=6.62,Kd=0.24uM

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003743 translation initiation factor activity

Biological Process

• GO:0006413 translational initiation

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:3m93, PDBe:3m93, PDBj:3m93
• PDBsum: 3m93
• PubMed: 21965542
• UniProt: Q6PKX2