Structure of PDB 4xja Chain A Binding Site BS02

Receptor Information
>4xja Chain A (length=658) Species: 170187 (Streptococcus pneumoniae TIGR4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ISPIFQGGSYQLNNKSIDISSLLLDKLSGESQTVVMKFKADKPNSLQALF
GLSNSKAGFKNNYFSIFMRDSGEIGVEIRDAQKGINYLFSRPASLWGKHK
GQAVENTLVFVSDSKDKTYTMYVNGIEVFSETVDTFLPISNINGIDKATL
GAVNREGKEHYLAKGSIDEISLFNKAISDQEVSTIPLSNPFQLIFQSGDS
TQANYFRIPTLYTLSSGRVLSSIDARYGGTHDSKSKINIATSYSDDNGKT
WSEPIFAMKFNDYEEQLVYWPRDNKLKNSQISGSASFIDSSIVEDKKSGK
TILLADVMPAGIGNNNANKADSGFKEINGHYYLKLKKNGDNDFRYTVREN
GVVYNETTNKPTNYTINDKYEVLEGGKSLTVEQYSVDFDSGSLRERHNGK
QVPMNVFYKDSLFKVTPTNYIAMTTSQNRGESWEQFKLLPPFLGEKHNGT
YLCPGQGLALKSSNRLIFATYTSGELTYLISDDSGQTWKKSSASIPFKNA
TAEAQMVELRDGVIRTFFRTTTGKIAYMTSRDSGETWSKVSYIDGIQQTS
YGTQVSAIKYSQLIDGKEAVILSTPNSRSGRKGGQLVVGLVNKEDDSIDW
KYHYGIDLPSYGYAYSAITELPNHHIGVLFEKYDSWSRNELHLSNVVQYI
DLEINDLT
Ligand information
Ligand IDSFJ
InChIInChI=1S/C11H17F2NO8/c1-3(16)14-5-7(19)9(12)11(13,10(20)21)22-8(5)6(18)4(17)2-15/h4-9,15,17-19H,2H2,1H3,(H,14,16)(H,20,21)/t4-,5-,6-,7-,8-,9-,11-/m1/s1
InChIKeyHMALKZAXODOYOP-DAXAGCIGSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(=O)N[CH]1[CH](O)[CH](F)[C](F)(O[CH]1[CH](O)[CH](O)CO)C(O)=O
CACTVS 3.385CC(=O)N[C@@H]1[C@@H](O)[C@@H](F)[C@@](F)(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O
OpenEye OEToolkits 1.9.2CC(=O)NC1C(C(C(OC1C(C(CO)O)O)(C(=O)O)F)F)O
ACDLabs 12.01FC1(OC(C(NC(=O)C)C(O)C1F)C(O)C(O)CO)C(=O)O
OpenEye OEToolkits 1.9.2CC(=O)N[C@@H]1[C@H]([C@H]([C@@](O[C@H]1[C@@H]([C@@H](CO)O)O)(C(=O)O)F)F)O
FormulaC11 H17 F2 N O8
Name(2R,3R,4R,5R,6R)-5-acetamido-2,3-difluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxylic acid;
(2R,3R,4R,5R,6R)-5-(acetylamino)-2,3-difluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxy lic acid;
2,3-difluoro-sialic acid;
5-acetamido-2,3-difluoro-3-hydroxy-6-[1,2,3-trihydroxypropyl]oxane-2-carboxylic acid
ChEMBLCHEMBL4128362
DrugBank
ZINCZINC000068203664
PDB chain4xja Chain A Residue 705 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4xja `The Hunt for Serendipitous Allosteric Sites: Discovery of a novel allosteric inhibitor of the bacterial sialidase NanB
Resolution1.98 Å
Binding residue
(original residue number in PDB)		R245 D270 I326 D327 N352 R557 R619 Y653
Binding residue
(residue number reindexed from 1)		R207 D232 I288 D289 N314 R519 R581 Y615
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D270 E541 Y653
Catalytic site (residue number reindexed from 1) D232 E503 Y615
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4xja, PDBe:4xja, PDBj:4xja
PDBsum4xja
PubMed
UniProtQ54727|NANB_STRPN Sialidase B (Gene Name=nanB)

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