Structure of PDB 7d7u Chain C Binding Site BS01

Receptor Information

>7d7u Chain C (length=135) Species: 9606 (Homo sapiens)

KQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQP
CFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTV
LGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGV

Ligand information

• Ligand ID: 8BR
• InChI: InChI=1S/C10H13BrN5O7P/c11-10-15-4-7(12)13-2-14-8(4)16(10)9-6(18)5(17)3(23-9)1-22-24(19,20)21/h2-3,5-6,9,17-18H,1H2,(H2,12,13,14)(H2,19,20,21)/t3-,5-,6-,9-/m1/s1
• InChIKey: DNPIJKNXFSPNNY-UUOKFMHZSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(c(n2)Br)C3C(C(C(O3)COP(=O)(O)O)O)O)N
  ACDLabs 10.04: Brc2nc1c(ncnc1n2C3OC(C(O)C3O)COP(=O)(O)O)N
  CACTVS 3.341: Nc1ncnc2n([CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O)c(Br)nc12
  CACTVS 3.341: Nc1ncnc2n([C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O)c(Br)nc12
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(c(n2)Br)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
• Formula: C10 H13 Br N5 O7 P
• Name: 8-BROMO-ADENOSINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL1230617
• DrugBank: DB03349
• ZINC: ZINC000013527361
• PDB chain: 7d7u Chain C Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7d7u siRNA potency enhancement via chemical modifications of nucleotide bases at the 5'-end of the siRNA guide strand.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): L522 G524 K525 T526 Y529 K533 Q545 C546 Q548 K570
• Binding residue (residue number reindexed from 1): L83 G85 K86 T87 Y90 K94 Q106 C107 Q109 K131
• Annotation score: 1
• Binding affinity: MOAD: Kd=100uM

Enzymatic activity

• Enzyme Commision number: 3.1.26.n2: argonaute-2.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding

External links

• PDB: RCSB:7d7u, PDBe:7d7u, PDBj:7d7u
• PDBsum: 7d7u
• PubMed: 33177188
• UniProt: Q9UKV8|AGO2_HUMAN Protein argonaute-2 (Gene Name=AGO2)