Structure of PDB 2ya8 Chain A Binding Site BS01

Receptor Information
>2ya8 Chain A (length=470) Species: 170187 (Streptococcus pneumoniae TIGR4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALTEKTDIFESGRNGNPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSS
DWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLV
QDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKG
AYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGDQLLGNIYFT
TNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPG
TGIVLRNGPHKGRILIPVYTTNNVSHLDGSQSSRVIYSDDHGKTWHAGEA
VNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQV
ATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKR
ENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTE
KGQNAYTLSFRKFNWEFLSK
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 chain2ya8 Chain A Residue 1777 [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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PDB2ya8 Structural Basis for Streptococcus Pneumoniae Nana Inhibition by Influenza Antivirals Zanamivir and Oseltamivir Carboxylate.
Resolution1.75 Å
Binding residue
(original residue number in PDB)
R332 D357 I401 D402 F550 R648 R706 Y737
Binding residue
(residue number reindexed from 1)
R26 D51 I95 D96 F244 R342 R400 Y431
Annotation score1
Binding affinityMOAD: Ki=1.77uM
PDBbind-CN: -logKd/Ki=5.75,Ki=1.77uM
BindingDB: Ki=1.77e+3nM
Enzymatic activity
Catalytic site (original residue number in PDB) S356 D357 E632 Y737
Catalytic site (residue number reindexed from 1) S50 D51 E326 Y431
Enzyme Commision number 3.2.1.18: exo-alpha-sialidase.
Gene Ontology
Molecular Function
GO:0004308 exo-alpha-sialidase activity

View graph for
Molecular Function
External links
PDB RCSB:2ya8, PDBe:2ya8, PDBj:2ya8
PDBsum2ya8
PubMed21514303
UniProtP62575|NANA_STREE Sialidase A (Gene Name=nanA)

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