Structure of PDB 4gzx Chain A Binding Site BS01

Receptor Information

>4gzx Chain A (length=388) Species: 119210 (H3N2 subtype)

AEYRNWSKPQCDITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPDKCYQ
FALGQGTTLNNVHSNNTVRGRTPYRTLLMNELGVPFHLGTKQVCIAWSSS
SCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVVSWSKEILRTQESECV
CINGTCTVVMTDGSASGKADTKILFIEEGKIVHTSTLSGSAQHVEECSCY
PRYPGVRCVCRDNWKGSNRPIVDINIKDHSIVSSYVCSGLVGDTPRKNDS
SSSSHCLDPNNEEGGHGVKGWAFDDGNDVWMGRTINETSRLGYETFKVIE
GWSNPKSKLQINRQVIVDRGNRSGYSGIFSVEGKSCINRCFYVELIRGRK
EETEVLWTSNSIVVFCGTSGTYGTGSWPDGADLNLMPI

Ligand information

• Ligand ID: SIA
• InChI: InChI=1S/C11H19NO9/c1-4(14)12-7-5(15)2-11(20,10(18)19)21-9(7)8(17)6(16)3-13/h5-9,13,15-17,20H,2-3H2,1H3,(H,12,14)(H,18,19)/t5-,6+,7+,8+,9+,11+/m0/s1
• InChIKey: SQVRNKJHWKZAKO-YRMXFSIDSA-N
• SMILES:
  CACTVS 3.341: CC(=O)N[CH]1[CH](O)C[C](O)(O[CH]1[CH](O)[CH](O)CO)C(O)=O
  OpenEye OEToolkits 1.5.0: CC(=O)NC1C(CC(OC1C(C(CO)O)O)(C(=O)O)O)O
  OpenEye OEToolkits 1.5.0: CC(=O)N[C@@H]1[C@H](C[C@@](O[C@H]1[C@@H]([C@@H](CO)O)O)(C(=O)O)O)O
  ACDLabs 10.04: O=C(O)C1(O)OC(C(O)C(O)CO)C(NC(=O)C)C(O)C1
  CACTVS 3.341: CC(=O)N[C@@H]1[C@@H](O)C[C@@](O)(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O
• Formula: C11 H19 N O9
• Name: N-acetyl-alpha-neuraminic acid;
  N-acetylneuraminic acid;
  sialic acid;
  alpha-sialic acid;
  O-SIALIC ACID
• ChEMBL: CHEMBL1234621
• DrugBank: DB03721
• ZINC: ZINC000004081651
• PDB chain: 4gzx Chain E Residue 2

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4gzx Influenza virus neuraminidases with reduced enzymatic activity that avidly bind sialic Acid receptors.
• Resolution: 2.45 Å
• Binding residue (original residue number in PDB): R118 E119 R152 R224 E276 R292 R371 Y406
• Binding residue (residue number reindexed from 1): R37 E38 R71 R143 E195 R211 R290 Y325
• Annotation score: 4
• Binding affinity: PDBbind-CN: -logKd/Ki=3.19,Kd=645uM

Enzymatic activity

• Catalytic site (original residue number in PDB): G151 E277 R292 R371 Y406
• Catalytic site (residue number reindexed from 1): G70 E196 R211 R290 Y325
• Enzyme Commision number: 3.2.1.18: exo-alpha-sialidase.

Gene Ontology

Molecular Function

• GO:0004308 exo-alpha-sialidase activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0046872 metal ion binding

Biological Process

• GO:0005975 carbohydrate metabolic process
• GO:0046761 viral budding from plasma membrane

Cellular Component

• GO:0016020 membrane
• GO:0020002 host cell plasma membrane
• GO:0033644 host cell membrane
• GO:0044423 virion component
• GO:0055036 virion membrane

External links

• PDB: RCSB:4gzx, PDBe:4gzx, PDBj:4gzx
• PDBsum: 4gzx
• PubMed: 23015718
• UniProt: K7N5N3