Structure of PDB 3hw4 Chain D Binding Site BS02

Receptor Information

>3hw4 Chain D (length=176) Species: 93838 (Influenza A virus (A/goose/Guangdong/1/1996(H5N1)))

PLGSMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCF
MYSRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIG
VTRREVHTYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARI
KTRLFTIRQEMASRGLWDSFRQSERG

Ligand information

• Ligand ID: TMP
• InChI: InChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
• InChIKey: GYOZYWVXFNDGLU-XLPZGREQSA-N
• SMILES:
  CACTVS 3.341: CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O
  CACTVS 3.341: CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
  ACDLabs 10.04: O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)COP(=O)(O)O
• Formula: C10 H15 N2 O8 P
• Name: THYMIDINE-5'-PHOSPHATE
• ChEMBL: CHEMBL394429
• DrugBank: DB01643
• ZINC: ZINC000001678872
• PDB chain: 3hw4 Chain D Residue 257

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3hw4 Nucleoside monophosphate complex structures of the endonuclease domain from the influenza virus polymerase PA subunit reveal the substrate binding site inside the catalytic center
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): A20 Y24 I38 H41 L42 E80 G81 D108 E119 K134
• Binding residue (residue number reindexed from 1): A24 Y28 I42 H45 L46 E59 G60 D87 E98 K113
• Annotation score: 4

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:3hw4, PDBe:3hw4, PDBj:3hw4
• PDBsum: 3hw4
• PubMed: 19587036
• UniProt: Q9Q0U9|PA_I96A0 Polymerase acidic protein (Gene Name=PA)