Structure of PDB 4xwh Chain A Binding Site BS01

Receptor Information
>4xwh Chain A (length=720) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DEAREAAAVRALVARLLGPGPAADFSVSVERALAAKPGLDTYSLGGGGAA
RVRVRGSTGVAAAAGLHRYLRDFCGCHVAWSGSQLRLPRPLPAVPGELTE
ATPNRYRYYQNVCTQSYSFVWWDWARWEREIDWMALNGINLALAWSGQEA
IWQRVYLALGLTQAEINEFFTGPAFLAWGRMGNLHTWDGPLPPSWHIKQL
YLQHRVLDQMRSFGMTPVLPAFAGHVPEAVTRVFPQVNVTKMGSWGHFNC
SYSCSFLLAPEDPIFPIIGSLFLRELIKEFGTDHIYGADTFNEMQPPSSE
PSYLAAATTAVYEAMTAVDTEAVWLLQGWLFQHQPQFWGPAQIRAVLGAV
PRGRLLVLDLFAESQPVYTRTASFQGQPFIWCMLHNFGGNHGLFGALEAV
NGGPEAARLFPNSTMVGTGMAPEGISQNEVVYSLMAELGWRKDPVPDLAA
WVTSFAARRYGVSHPDAGAAWRLLLRSVYNCSGEACRGHNRSPLVRRPSL
QMNTSIWYNRSDVFEAWRLLLTSAPSLATSPAFRYDLLDLTRQAVQELVS
LYYEEARSAYLSKELASLLRAGGVLAYELLPALDEVLASDSRFLLGSWLE
QARAAAVSEAEADFYEQNSRYQLTLWGPEGNILDYANKQLAGLVANYYTP
RWRLFLEALVDSVAQGIPFQQHQFDKNVFQLEQAFVLSKQRYPSQPRGDT
VDLAKKIFLKYYPRWVAGSW
Ligand information
Ligand IDXYL
InChIInChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4+,5+
InChIKeyHEBKCHPVOIAQTA-SCDXWVJYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C([C@@H](C([C@@H](CO)O)O)O)O
OpenEye OEToolkits 1.5.0C(C(C(C(CO)O)O)O)O
CACTVS 3.341OC[CH](O)[CH](O)[CH](O)CO
CACTVS 3.341OC[C@H](O)[C@@H](O)[C@H](O)CO
ACDLabs 10.04OC(CO)C(O)C(O)CO
FormulaC5 H12 O5
NameXylitol;
D-Xylitol
ChEMBLCHEMBL96783
DrugBankDB11195
ZINCZINC000100018612
PDB chain4xwh Chain A Residue 2014 [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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PDB4xwh Structural characterization of the alpha-N-acetylglucosaminidase, a key enzyme in the pathogenesis of Sanfilippo syndrome B.
Resolution2.32 Å
Binding residue
(original residue number in PDB)		A87 H90 R94 N160 A459 E460 W463
Binding residue
(residue number reindexed from 1)		A64 H67 R71 N137 A436 E437 W440
Annotation score4
Enzymatic activity
Enzyme Commision number 3.2.1.50: alpha-N-acetylglucosaminidase.
Gene Ontology
Molecular Function
GO:0004561 alpha-N-acetylglucosaminidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
Biological Process
GO:0001573 ganglioside metabolic process
GO:0001774 microglial cell activation
GO:0001889 liver development
GO:0001944 vasculature development
GO:0003158 endothelium development
GO:0003170 heart valve development
GO:0003183 mitral valve morphogenesis
GO:0003220 left ventricular cardiac muscle tissue morphogenesis
GO:0006029 proteoglycan metabolic process
GO:0006801 superoxide metabolic process
GO:0006914 autophagy
GO:0006954 inflammatory response
GO:0007028 cytoplasm organization
GO:0007030 Golgi organization
GO:0007033 vacuole organization
GO:0007040 lysosome organization
GO:0007399 nervous system development
GO:0007507 heart development
GO:0007626 locomotory behavior
GO:0008340 determination of adult lifespan
GO:0009100 glycoprotein metabolic process
GO:0009611 response to wounding
GO:0010467 gene expression
GO:0014004 microglia differentiation
GO:0016485 protein processing
GO:0021675 nerve development
GO:0021680 cerebellar Purkinje cell layer development
GO:0022008 neurogenesis
GO:0030200 heparan sulfate proteoglycan catabolic process
GO:0030201 heparan sulfate proteoglycan metabolic process
GO:0030202 heparin metabolic process
GO:0030203 glycosaminoglycan metabolic process
GO:0030534 adult behavior
GO:0031069 hair follicle morphogenesis
GO:0032496 response to lipopolysaccharide
GO:0032963 collagen metabolic process
GO:0034142 toll-like receptor 4 signaling pathway
GO:0034285 response to disaccharide
GO:0034599 cellular response to oxidative stress
GO:0035633 maintenance of blood-brain barrier
GO:0035640 exploration behavior
GO:0035904 aorta development
GO:0035909 aorta morphogenesis
GO:0042445 hormone metabolic process
GO:0042474 middle ear morphogenesis
GO:0042982 amyloid precursor protein metabolic process
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0044242 cellular lipid catabolic process
GO:0045475 locomotor rhythm
GO:0046548 retinal rod cell development
GO:0048143 astrocyte activation
GO:0048708 astrocyte differentiation
GO:0055013 cardiac muscle cell development
GO:0060041 retina development in camera-type eye
GO:0060119 inner ear receptor cell development
GO:0060173 limb development
GO:0060586 multicellular organismal-level iron ion homeostasis
GO:0061744 motor behavior
GO:0071407 cellular response to organic cyclic compound
GO:0097577 sequestering of iron ion
GO:0097696 cell surface receptor signaling pathway via STAT
GO:0099022 vesicle tethering
GO:0150076 neuroinflammatory response
GO:1901135 carbohydrate derivative metabolic process
GO:1904389 rod bipolar cell differentiation
GO:1904390 cone retinal bipolar cell differentiation
Cellular Component
GO:0005764 lysosome
GO:0005773 vacuole
GO:0043202 lysosomal lumen
GO:0070062 extracellular exosome

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4xwh, PDBe:4xwh, PDBj:4xwh
PDBsum4xwh
PubMed30802506
UniProtP54802|ANAG_HUMAN Alpha-N-acetylglucosaminidase (Gene Name=NAGLU)

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