Structure of PDB 6k35 Chain B Binding Site BS01

Receptor Information
>6k35 Chain B (length=640) Species: 669 (Vibrio harveyi) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSEYRVDLVVLSEQKQNCRFGLTFHNLSDQDLNSWGLTFAFDRYILPDSV
SNGQLTQIGSFCTLKPEGIVLAANHHYYCEFSIGSNPFRYYSDGFNEAMI
DFVVDGQPQRAQVDVTPIVLASPYRERSDIPASLTHAQPLLPKPNHIEVS
DHSFTFDEQAGVAIYTDLANSAKAWLLEELQRIHQFTLSSSNSGKIIFKS
NPTLDEGAYKLKVSEESIKIEAGSSSGFTHACATLLQLLKRDEATKTMEA
VCCSIIDSPRFRYRGMMLDCARHFHSVEQVKRLINLLAHYKLNTFHWHLT
DDEGWRVEIKSLPQLTEIGAWRGIDETIEPQYTHLSQRYGGFYTQEEIRD
VIAFAEQRGITIIPEIDVPGHCRAAIKSLPHLLIEAEDTTEYRSIQHYND
NVINPALPGSYEFIDKVLEEIAALFPAPYVHIGADEVPNGVWSKSPACQA
LMEQLGYTDYKELQGHFLRHAEDKLRKLGKRMLGWEEAQHGNKVSKDTVI
YSWLSEEAALNCARQGFDVVLQPAQTTYLDMTQDYAPEEPGVDWANPLPL
EKAYNYEPLAEVPADDPIRKRIWGIQTALWCEIINNPSRMDYMIFPRLTA
MAEACWTEKQHRDWTDYLSRLKGHLPLLDLQGVNYRKPWK
Ligand information
Ligand IDNGT
InChIInChI=1S/C8H13NO4S/c1-3-9-5-7(12)6(11)4(2-10)13-8(5)14-3/h4-8,10-12H,2H2,1H3/t4-,5-,6-,7-,8-/m1/s1
InChIKeyDRHXTSWSUAJOJZ-FMDGEEDCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=NC2C(C(C(OC2S1)CO)O)O
ACDLabs 10.04N1=C(SC2OC(C(O)C(O)C12)CO)C
OpenEye OEToolkits 1.5.0CC1=N[C@@H]2[C@H]([C@@H]([C@H](O[C@@H]2S1)CO)O)O
CACTVS 3.341CC1=N[CH]2[CH](O)[CH](O)[CH](CO)O[CH]2S1
CACTVS 3.341CC1=N[C@@H]2[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]2S1
FormulaC8 H13 N O4 S
Name3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL
ChEMBLCHEMBL257158
DrugBankDB03747
ZINCZINC000016051892
PDB chain6k35 Chain B Residue 701 [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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PDB6k35 NAG-thiazoline is a potent inhibitor of the Vibrio campbellii GH20 beta-N-Acetylglucosaminidase.
Resolution2.36 Å
Binding residue
(original residue number in PDB)		R274 D437 E438 W487 W505 Y530 D532 W546 W582 E584
Binding residue
(residue number reindexed from 1)		R272 D435 E436 W485 W503 Y528 D530 W544 W580 E582
Annotation score1
Binding affinityMOAD: ic50=11.9uM
Enzymatic activity
Catalytic site (original residue number in PDB) D437 E438
Catalytic site (residue number reindexed from 1) D435 E436
Enzyme Commision number 3.2.1.52: beta-N-acetylhexosaminidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004563 beta-N-acetylhexosaminidase activity
GO:0016231 beta-N-acetylglucosaminidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0030203 glycosaminoglycan metabolic process
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6k35, PDBe:6k35, PDBj:6k35
PDBsum6k35
PubMed32145141
UniProtD9ISE0

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