Structure of PDB 5l17 Chain A Binding Site BS02

Receptor Information

>5l17 Chain A (length=388) Species: 1332244 (Influenza A virus (A/Shanghai/02/2013(H7N9)))

RNFNNLTKGLCTINSWHIYGKDNAVRIGESSDVLVTREPYVSCDPDECRF
YALSQGTTIRGKHSNGTIHDRSQYRALISWPLSSPPTVYNSRVECIGWSS
TSCHDGKSRMSICISGPNNNASAVVWYNRRPVAEINTWARNILRTQESEC
VCHNGVCPVVFTDGSATGPADTRIYYFKEGKILKWESLTGTAKHIEECSC
YGERTGITCTCRDNWQGSNRPVIQIDPVAMTHTSQYICSPVLTDNPRPND
PNIGKCNDPYPGNNNNGVKGFSYLDGANTWLGRTISTASRSGYEMLKVPN
ALTDDRSKPIQGQTIVLNADWSGYSGSFMDYWAEGDCYRACFYVELIRGR
PKEDKVWWTSNSIVSMCSSTEFLGQWNWPDGAKIEYFL

Ligand information

• Ligand ID: ZMR
• InChI: InChI=1S/C12H20N4O7/c1-4(18)15-8-5(16-12(13)14)2-7(11(21)22)23-10(8)9(20)6(19)3-17/h2,5-6,8-10,17,19-20H,3H2,1H3,(H,15,18)(H,21,22)(H4,13,14,16)/t5-,6+,8+,9+,10+/m0/s1
• InChIKey: ARAIBEBZBOPLMB-UFGQHTETSA-N
• SMILES:
  CACTVS 3.385: CC(=O)N[CH]1[CH](NC(N)=N)C=C(O[CH]1[CH](O)[CH](O)CO)C(O)=O
  ACDLabs 12.01: C(=O)(O)C1=CC(C(NC(=O)C)C(O1)C(O)C(O)CO)N\C(=N)N
  CACTVS 3.385: CC(=O)N[C@@H]1[C@@H](NC(N)=N)C=C(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O
  OpenEye OEToolkits 2.0.7: CC(=O)NC1C(C=C(OC1C(C(CO)O)O)C(=O)O)NC(=N)N
  OpenEye OEToolkits 2.0.7: [H]/N=C(\N)/N[C@H]1C=C(O[C@H]([C@@H]1NC(=O)C)[C@@H]([C@@H](CO)O)O)C(=O)O
• Formula: C12 H20 N4 O7
• Name: ZANAMIVIR;
  4-GUANIDINO-2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID;
  4-guanidino-Neu5Ac2en;
  MODIFIED SIALIC ACID
• ChEMBL: CHEMBL222813
• DrugBank: DB00558
• ZINC: ZINC000003918138
• PDB chain: 5l17 Chain A Residue 512

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5l17 Drug Susceptibility Evaluation of an Influenza A(H7N9) Virus by Analyzing Recombinant Neuraminidase Proteins.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): R119 E120 D152 R153 W180 R226 E229 A248 E278 R294 R372 Y406
• Binding residue (residue number reindexed from 1): R37 E38 D70 R71 W98 R144 E147 A166 E196 R212 R290 Y324
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=9.30,IC50=0.5nM

Enzymatic activity

• Catalytic site (original residue number in PDB): D152 E279 R294 R372 Y406
• Catalytic site (residue number reindexed from 1): D70 E197 R212 R290 Y324
• Enzyme Commision number: 3.2.1.18: exo-alpha-sialidase.

Gene Ontology

Molecular Function

• GO:0004308 exo-alpha-sialidase activity

Biological Process

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

Cellular Component

• GO:0016020 membrane
• GO:0033644 host cell membrane
• GO:0055036 virion membrane

External links

• PDB: RCSB:5l17, PDBe:5l17, PDBj:5l17
• PDBsum: 5l17
• PubMed: 28934455
• UniProt: R4NFR6