Structure of PDB 6eks Chain A Binding Site BS04

Receptor Information
>6eks Chain A (length=749) Species: 243277 (Vibrio cholerae O1 biovar El Tor str. N16961) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALFDYNATGDTFDSPAKQGWMQDNTNNGSGVLTNAMPAWLVQGIGGRAQW
TYSLSTNQHAQASSFGWRMTTEMKVLSGGMITNYYANGTQRVLPIISLDS
SGNLVVEFEGQTGRTVLATGTAATEYHKFELVFLPGSNPSASFYFDGKLI
RDNIQPTASKQNMIVWGNGSSNTDGVAAYRDIKFEIQGDVIFRGPDRIPS
IVASSVTPGVVTAFAEKRVGGGDPGALSNTNDIITRTSRDGGITWDTELN
LTEQINVSDEFDFSDPRPIYDPSSNTVLVSYARWPTDAAQNGDRIKPWMP
NGIFYSVYDVASGNWQAPIDVTDQVKERSFQIAGWGGSELYRRNTSLNSQ
QDWQSNAKIRIVDGAANQIQVADGSRKYVVTLSIDESGGLVANLNGVSAP
IILQSEHAKVHSFHDYELQYSALNHTTTLFVDGQQITTWAGEVSQENNIQ
FGNADAQIDGRLHVQKIVLTQQGHNLVEFDAFYLAQQTPEVEKDLEKLGW
TKIKTGNTMSLYGNASVNPGPGHGITLTRQQNISGSQNGRLIYPAIVLDR
FFLNVMSIYSDDGGSNWQTGSTLPIPFRWKSSSILETLEPSEADMVELQN
GDLLLTARLDFNQIVNGVNYSPRQQFLSKDGGITWSLLEANNANVFSNIS
TGTVDASITRFEQSDGSHFLLFTNPQGNPAGTNGRQNLGLWFSFDEGVTW
KGPIQLVNGASAYSDIYQLDSENAIVIVETDNSNMRILRMPITLLKQKL
Ligand information
Ligand IDG39
InChIInChI=1S/C14H24N2O4/c1-4-10(5-2)20-12-7-9(14(18)19)6-11(15)13(12)16-8(3)17/h7,10-13H,4-6,15H2,1-3H3,(H,16,17)(H,18,19)/t11-,12+,13+/m0/s1
InChIKeyNENPYTRHICXVCS-YNEHKIRRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CCC(CC)OC1C=C(CC(C1NC(=O)C)N)C(=O)O
OpenEye OEToolkits 1.7.0CCC(CC)O[C@@H]1C=C(C[C@@H]([C@H]1NC(=O)C)N)C(=O)O
CACTVS 3.370CCC(CC)O[C@@H]1C=C(C[C@H](N)[C@H]1NC(C)=O)C(O)=O
CACTVS 3.370CCC(CC)O[CH]1C=C(C[CH](N)[CH]1NC(C)=O)C(O)=O
ACDLabs 12.01O=C(O)C1=CC(OC(CC)CC)C(NC(=O)C)C(N)C1
FormulaC14 H24 N2 O4
Name(3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid;
Oseltamivir carboxylate
ChEMBLCHEMBL674
DrugBankDB02600
ZINCZINC000003929509
PDB chain6eks Chain A Residue 908 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6eks Different Inhibitory Potencies of Oseltamivir Carboxylate, Zanamivir, and Several Tannins on Bacterial and Viral Neuraminidases as Assessed in a Cell-Free Fluorescence-Based Enzyme Inhibition Assay.
Resolution1.87 Å
Binding residue
(original residue number in PDB)		R250 D276 Q343 E645 R661 D663 R738 Y766
Binding residue
(residue number reindexed from 1)		R197 D223 Q290 E592 R608 D610 R685 Y713
Annotation score1
Binding affinityMOAD: ic50=144uM
PDBbind-CN: -logKd/Ki=3.84,IC50=144uM
Enzymatic activity
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:0033691 sialic acid binding
Biological Process
GO:0006689 ganglioside catabolic process
GO:0009313 oligosaccharide catabolic process
Cellular Component
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0016020 membrane
GO:0043231 intracellular membrane-bounded organelle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6eks, PDBe:6eks, PDBj:6eks
PDBsum6eks
PubMed29149072
UniProtP0C6E9|NANH_VIBCH Sialidase (Gene Name=nanH)

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