Structure of PDB 5kky Chain B Binding Site BS01

Receptor Information
>5kky Chain B (length=470) Species: 1313 (Streptococcus pneumoniae) [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 ID6UD
InChIInChI=1S/C11H20N4O7/c1-4(16)14-8-5(17)2-7(11(20)21)22-10(8)9(19)6(18)3-13-15-12/h2,5-6,8-10,13,15,17-19H,3,12H2,1H3,(H,14,16)(H,20,21)/t5-,6+,8+,9+,10+/m0/s1
InChIKeyFQISBZMFUOAQIB-UFGQHTETSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(=O)NC1C(C=C(OC1C(C(CNNN)O)O)C(=O)O)O
CACTVS 3.385CC(=O)N[CH]1[CH](O)C=C(O[CH]1[CH](O)[CH](O)CNNN)C(O)=O
CACTVS 3.385CC(=O)N[C@@H]1[C@@H](O)C=C(O[C@H]1[C@H](O)[C@H](O)CNNN)C(O)=O
OpenEye OEToolkits 2.0.7CC(=O)N[C@@H]1[C@H](C=C(O[C@H]1[C@@H]([C@@H](CNNN)O)O)C(=O)O)O
ACDLabs 12.01C(C=1OC(C(C(C=1)O)NC(=O)C)C(C(O)CNNN)O)(=O)O
FormulaC11 H20 N4 O7
Name5-acetamido-2,6-anhydro-3,5,9-trideoxy-9-triazan-1-yl-D-glycero-D-galacto-non-2-enonic acid;
(2~{R},3~{R},4~{S})-3-acetamido-2-[(1~{R},2~{R})-3-(2-azanylhydrazinyl)-1,2-bis(oxidanyl)propyl]-4-oxidanyl-3,4-dihydro -2~{H}-pyran-6-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain5kky Chain B Residue 902 [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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PDB5kky Synthesis of selective inhibitors against S. pneumoniae and V. cholerae sialidases
Resolution2.393 Å
Binding residue
(original residue number in PDB)
R332 I401 D402 Y575 Q587 R648 Y680 R706 Y737
Binding residue
(residue number reindexed from 1)
R26 I95 D96 Y269 Q281 R342 Y374 R400 Y431
Annotation score1
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:5kky, PDBe:5kky, PDBj:5kky
PDBsum5kky
PubMed
UniProtP62575|NANA_STREE Sialidase A (Gene Name=nanA)

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