Structure of PDB 5y0v Chain A Binding Site BS01

Receptor Information
>5y0v Chain A (length=572) Species: 93504 (Ostrinia furnacalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EDVVWRWSCDNGKCVKLKNDPRSSEPALSLEACKMFCNEYGLLWPRPTGE
ADLGNFLSKINLNSIEVKILKKGATDDLMEAAAKRFKEQVSLAIPRGSTP
KLTGKAVDVYLVNENPNEKAFSLEMDESYGLRVSPSGADRVNATITANSF
FGMRHGLETLSQLFVFDDIRDHLLMVRDVNISDKPVYPYRGILLDTARNY
YSIESIKRTIEAMAAVKLNTDHWHITDSQSFPFVTTKRPNLYKFGALSPQ
KVYTKAAIREVVRFGLERGVRVLPEFDAPAHVGEGWQDTDLTVCFKAEPW
KSYCVEPPCGQLNPTKDELYQYLEDIYSDMAEVFDTTDIFHMGGDEVSEA
CWNSSDSIQNFMMQNRWDLDKESFLKLWNYFQQKAQDKAYKAFGKKLPLI
LWTSTLTNYKHIDDYLNKDDYIIQVWTTGVDPQIKGLLEKGYRLIMSNYD
ALYFDCGYGAWVGAGNNWCSPYIGWQKVYDNSPAVIALEHRDQVLGGEAA
LWSEQSDTSTLDGRLWPRAAALAERLWAEPATSWQDAEYRMLHIRERFVR
MGIQAESLQPEWCYQNEGYCYS
Ligand information
Ligand IDBER
InChIInChI=1S/C20H18NO4/c1-22-17-4-3-12-7-16-14-9-19-18(24-11-25-19)8-13(14)5-6-21(16)10-15(12)20(17)23-2/h3-4,7-10H,5-6,11H2,1-2H3/q+1
InChIKeyYBHILYKTIRIUTE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0COc1ccc2cc-3[n+](cc2c1OC)CCc4c3cc5c(c4)OCO5
ACDLabs 10.04O1c2c(OC1)cc5c(c2)c4cc3ccc(OC)c(OC)c3c[n+]4CC5
CACTVS 3.341COc1ccc2cc3c4cc5OCOc5cc4CC[n+]3cc2c1OC
FormulaC20 H18 N O4
NameBERBERINE
ChEMBLCHEMBL295124
DrugBankDB04115
ZINCZINC000003779067
PDB chain5y0v 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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PDB5y0v Glycoside hydrolase family 18 and 20 enzymes are novel targets of the traditional medicine berberine.
Resolution2.423 Å
Binding residue
(original residue number in PDB)		V327 W448 W483 W490
Binding residue
(residue number reindexed from 1)		V305 W426 W461 W468
Annotation score1
Binding affinityMOAD: Ki=12uM
Enzymatic activity
Catalytic site (original residue number in PDB) D367 E368
Catalytic site (residue number reindexed from 1) D345 E346
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:0000272 polysaccharide catabolic process
GO:0005975 carbohydrate metabolic process
GO:0006032 chitin catabolic process
GO:0006517 protein deglycosylation
GO:0006689 ganglioside catabolic process
GO:0030203 glycosaminoglycan metabolic process
Cellular Component
GO:0005764 lysosome
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5y0v, PDBe:5y0v, PDBj:5y0v
PDBsum5y0v
PubMed30135205
UniProtQ06GJ0|HEXC_OSTFU Chitooligosaccharidolytic beta-N-acetylglucosaminidase

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