Structure of PDB 4yw2 Chain A Binding Site BS01

Receptor Information
>4yw2 Chain A (length=659) Species: 170187 (Streptococcus pneumoniae TIGR4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ETPVLEKNNVTLTGGGENVTKELKDKFTSGDFTVVIKYNQSSEKGLQALF
GISNSKPGQQNSYVDVFLRDNGELGMEARDTSSNKNNLVSRPASVWGKYK
QEAVTNTVAVVADSVKKTYSLYANGTKVVEKKVDNFLNIKDIKGIDYYML
GGVKRAGKTAFGFNGTLENIKFFNSALDEETVKKMTTNAVTGHLIYTAND
TTGSNYFRIPVLYTFSNGRVFSSIDARYGGTHDFLNKINIATSYSDDNGK
TWTKPKLTLAFDDFAPVPLEWPREVGGRDLQISGGATYIDSVIVEKKNKQ
VLMFADVMPAGVSFREATRKDSGYKQIDGNYYLKLRKQGDTDYNYTIREN
GTVYDDRTNRPTEFSVDKNFGIKQNGNYLTVEQYSVSFENNKKTEYRNGT
KVHMNIFYKDALFKVVPTNYIAYISSNDHGESWSAPTLLPPIMGLNRNAP
YLGPGRGIIESSTGRILIPSYTGKESAFIYSDDNGASWKVKVVPLPSSWS
AEAQFVELSPGVIQAYMRTNNGKIAYLTSKDAGTTWSAPEYLKFVSNPSY
GTQLSIINYSQLIDGKKAVILSTPNSTNGRKHGQIWIGLINDDNTIDWRY
HHDVDYSNYGYSYSTLTELPNHEIGLMFEKFDSWSRNELHMKNVVPYITF
KIEDLKKNL
Ligand information
Ligand IDSIA
InChIInChI=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
InChIKeySQVRNKJHWKZAKO-YRMXFSIDSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(=O)N[CH]1[CH](O)C[C](O)(O[CH]1[CH](O)[CH](O)CO)C(O)=O
OpenEye OEToolkits 1.5.0CC(=O)NC1C(CC(OC1C(C(CO)O)O)(C(=O)O)O)O
OpenEye OEToolkits 1.5.0CC(=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 10.04O=C(O)C1(O)OC(C(O)C(O)CO)C(NC(=O)C)C(O)C1
CACTVS 3.341CC(=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
FormulaC11 H19 N O9
NameN-acetyl-alpha-neuraminic acid;
N-acetylneuraminic acid;
sialic acid;
alpha-sialic acid;
O-SIALIC ACID
ChEMBLCHEMBL1234621
DrugBankDB03721
ZINCZINC000004081651
PDB chain4yw2 Chain C Residue 2 [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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PDB4yw2 Streptococcus pneumoniae NanC: STRUCTURAL INSIGHTS INTO THE SPECIFICITY AND MECHANISM OF A SIALIDASE THAT PRODUCES A SIALIDASE INHIBITOR.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		L128 F149 R151 E159 R161 R237
Binding residue
(residue number reindexed from 1)		L46 F67 R69 E77 R79 R155
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=2.80,Kd=1.6mM
Enzymatic activity
Catalytic site (original residue number in PDB) D315 E584 Y695
Catalytic site (residue number reindexed from 1) D233 E502 Y613
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
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006689 ganglioside catabolic process
GO:0009313 oligosaccharide catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0016020 membrane
GO:0043231 intracellular membrane-bounded organelle

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4yw2, PDBe:4yw2, PDBj:4yw2
PDBsum4yw2
PubMed26370075
UniProtA0A0H2UQE4

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