Structure of PDB 4xil Chain A Binding Site BS01

Receptor Information
>4xil 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 IDOPX
InChIInChI=1S/C12H23NO5S/c14-10-6-12(7-11(10)15,19(16,17)18)8-13-9-4-2-1-3-5-9/h9-11,13-15H,1-8H2,(H,16,17,18)/t10-,11+,12-
InChIKeyRMLVAYWMDDDXFB-ZSBIGDGJSA-N
SMILES
SoftwareSMILES
CACTVS 3.370O[C@@H]1C[C@](CNC2CCCCC2)(C[C@@H]1O)[S](O)(=O)=O
OpenEye OEToolkits 1.7.6C1CCC(CC1)NCC2(CC(C(C2)O)O)S(=O)(=O)O
OpenEye OEToolkits 1.7.6C1CCC(CC1)NCC2(C[C@H]([C@H](C2)O)O)S(=O)(=O)O
CACTVS 3.370O[CH]1C[C](CNC2CCCCC2)(C[CH]1O)[S](O)(=O)=O
ACDLabs 12.01O=S(=O)(O)C1(CC(O)C(O)C1)CNC2CCCCC2
FormulaC12 H23 N O5 S
Name(1s,3R,4S)-1-[(cyclohexylamino)methyl]-3,4-dihydroxycyclopentanesulfonic acid
ChEMBL
DrugBank
ZINCZINC000263620979
PDB chain4xil Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4xil `The Hunt for Serendipitous Allosteric Sites: Discovery of a novel allosteric inhibitor of the bacterial sialidase NanB
Resolution1.9 Å
Binding residue
(original residue number in PDB)		Y250 T251 Q494 K499 E658
Binding residue
(residue number reindexed from 1)		Y212 T213 Q456 K461 E620
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
View graph for
Cellular Component
External links
PDB RCSB:4xil, PDBe:4xil, PDBj:4xil
PDBsum4xil
PubMed
UniProtQ54727|NANB_STRPN Sialidase B (Gene Name=nanB)

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