Structure of PDB 5wdw Chain A Binding Site BS03

Receptor Information

>5wdw Chain A (length=180) Species: 641501 (Influenza A virus (A/California/04/2009(H1N1)))

RGSHMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCF
MYSDGGSKHRFEIIEGRDRIMAWTVVNSICNTTGVEKPKFLPDLYDYKEN
RFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDE
ESRARIKTRLFTIRQEMASRSLWDSFRQSE

Ligand information

• Ligand ID: 8KU
• InChI: InChI=1S/C26H25ClN4O5S/c27-17-7-2-4-10-20(17)37-14-21(32)31-11-5-8-18(31)24-29-22(23(33)26(35)30-24)25(34)28-13-16-12-15-6-1-3-9-19(15)36-16/h1-4,6-7,9-10,16,18,33H,5,8,11-14H2,(H,28,34)(H,29,30,35)/t16-,18-/m0/s1
• InChIKey: DAFZALMPATYNDF-WMZOPIPTSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: c1ccc2c(c1)CC(O2)CNC(=O)C3=C(C(=O)NC(=N3)C4CCCN4C(=O)CSc5ccccc5Cl)O
  CACTVS 3.385: OC1=C(N=C(NC1=O)[C@@H]2CCCN2C(=O)CSc3ccccc3Cl)C(=O)NC[C@@H]4Cc5ccccc5O4
  CACTVS 3.385: OC1=C(N=C(NC1=O)[CH]2CCCN2C(=O)CSc3ccccc3Cl)C(=O)NC[CH]4Cc5ccccc5O4
  ACDLabs 12.01: C3(=O)C(O)=C(C(=O)NCC2Cc1ccccc1O2)N=C(N3)C4CCCN4C(CSc5ccccc5Cl)=O
  OpenEye OEToolkits 2.0.6: c1ccc2c(c1)C[C@H](O2)CNC(=O)C3=C(C(=O)NC(=N3)[C@@H]4CCCN4C(=O)CSc5ccccc5Cl)O
• Formula: C26 H25 Cl N4 O5 S
• Name: 2-[(2S)-1-{[(2-chlorophenyl)sulfanyl]acetyl}pyrrolidin-2-yl]-N-{[(2S)-2,3-dihydro-1-benzofuran-2-yl]methyl}-5-hydroxy-6-oxo-1,6-dihydropyrimidine-4-carboxamide;
  SRI-30027
• PDB chain: 5wdw Chain A Residue 203

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5wdw Protein-Structure Assisted Optimization of 4,5-Dihydroxypyrimidine-6-Carboxamide Inhibitors of Influenza Virus Endonuclease.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): Y24 K34 A37 I38 H41 E80 D108
• Binding residue (residue number reindexed from 1): Y28 K38 A41 I42 H45 E65 D93
• Annotation score: 1
• Binding affinity: MOAD: Ki=0.29uM
  PDBbind-CN: -logKd/Ki=6.54,Ki=0.29uM

Enzymatic activity

• Enzyme Commision number: 3.1.-.-

Gene Ontology

Molecular Function

• GO:0003723 RNA binding

Biological Process

• GO:0039694 viral RNA genome replication

External links

• PDB: RCSB:5wdw, PDBe:5wdw, PDBj:5wdw
• PDBsum: 5wdw
• PubMed: 29215062
• UniProt: C3W5S0