Structure of PDB 8dpj Chain A Binding Site BS04

Receptor Information

>8dpj Chain A (length=180) Species: 11320 (Influenza A virus)

RGSHMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCF
MYSDGGSKHRFEIIEGRDRIMAWTVVNSICNTTGVEKPKFLPDLYDYKEN
RFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDE
ESRARIKTRLFTIRQEMASRSLWDSFRQSE

Ligand information

• Ligand ID: SE9
• InChI: InChI=1S/C20H17F3N4O4/c1-31-14-9-11(5-7-24-14)6-8-25-18(29)15-16(28)19(30)27-17(26-15)12-3-2-4-13(10-12)20(21,22)23/h2-5,7,9-10,28H,6,8H2,1H3,(H,25,29)(H,26,27,30)
• InChIKey: CJUKCSPPUSTPJP-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: COc1cc(ccn1)CCNC(=O)C2=C(C(=O)NC(=N2)c3cccc(c3)C(F)(F)F)O
  CACTVS 3.385: COc1cc(CCNC(=O)C2=C(O)C(=O)NC(=N2)c3cccc(c3)C(F)(F)F)ccn1
  ACDLabs 12.01: OC1=C(N=C(NC1=O)c1cccc(c1)C(F)(F)F)C(=O)NCCc1ccnc(OC)c1
• Formula: C20 H17 F3 N4 O4
• Name: (2P)-5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-6-oxo-2-[3-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-4-carboxamide
• PDB chain: 8dpj Chain A Residue 204

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8dpj Chemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential.
• Resolution: 2.45 Å
• Binding residue (original residue number in PDB): Y24 K34 A37 I38 H41 E119 R124
• Binding residue (residue number reindexed from 1): Y28 K38 A41 I42 H45 E104 R109
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0003723 RNA binding

Biological Process

• GO:0039694 viral RNA genome replication

External links

• PDB: RCSB:8dpj, PDBe:8dpj, PDBj:8dpj
• PDBsum: 8dpj
• PubMed: 36603507
• UniProt: C6H0Y9