Structure of PDB 8k7k Chain B Binding Site BS01

Receptor Information
>8k7k Chain B (length=392) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LDNGLARTPTMGWLHWERFMCNLDCQEEPDSCISEKLFMEMAELMVSEGW
KDAGYEYLCIDDCWMAPQRDSEGRLQADPQRFPHGIRQLANYVHSKGLKL
GIYADVGNKTCAGFPGSFGYYDIDAQTFADWGVDLLKFDGCYCDSLENLA
DGYKHMSLALNRTGRSIVYSCEWPLYMWPFQKPNYTEIRQYCNHWRNFAD
IDDSWKSIKSILDWTSFNQERIVDVAGPGGWNDPDMLVIGNFGLSWNQQV
TQMALWAIMAAPLFMSNDLRHISPQAKALLQDKDVIAINQDPLGKQGYQL
RQGDNFEVWERPLSGLAWAVAMINRQEIGGPRSYTIAVASLGKGVACNPA
CFITQLLPVKRKLGFYEWTSRLRSHINPTGTVLLQLENTMQM
Ligand information
Ligand IDVNQ
InChIInChI=1S/C7H15NO4/c1-8-4(2-9)6(11)7(12)5(8)3-10/h4-7,9-12H,2-3H2,1H3/t4-,5-,6-,7+/m1/s1
InChIKeyYWBPEHFIHKFMMC-GBNDHIKLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CN1C(C(C(C1CO)O)O)CO
CACTVS 3.385CN1[C@H](CO)[C@H](O)[C@H](O)[C@H]1CO
OpenEye OEToolkits 2.0.7CN1[C@@H]([C@H]([C@H]([C@H]1CO)O)O)CO
CACTVS 3.385CN1[CH](CO)[CH](O)[CH](O)[CH]1CO
FormulaC7 H15 N O4
Name(2~{R},3~{S},4~{R},5~{R})-2,5-bis(hydroxymethyl)-1-methyl-pyrrolidine-3,4-diol
ChEMBL
DrugBank
ZINC
PDB chain8k7k Chain B Residue 502 [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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PDB8k7k Mechanistic Insights into Dibasic Iminosugars as pH-Selective Pharmacological Chaperones to Stabilize Human alpha-Galactosidase.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		W47 D92 D93 Y134 C142 K168 D170 E203 D231
Binding residue
(residue number reindexed from 1)		W16 D61 D62 Y103 C111 K137 D139 E172 D200
Annotation score1
Enzymatic activity
Enzyme Commision number 3.2.1.22: alpha-galactosidase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004557 alpha-galactosidase activity
GO:0005102 signaling receptor binding
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0016936 galactoside binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006629 lipid metabolic process
GO:0009311 oligosaccharide metabolic process
GO:0016139 glycoside catabolic process
GO:0019915 lipid storage
GO:0030168 platelet activation
GO:0030431 sleep
GO:0031133 regulation of axon diameter
GO:0045019 negative regulation of nitric oxide biosynthetic process
GO:0046477 glycosylceramide catabolic process
GO:0046479 glycosphingolipid catabolic process
GO:0051001 negative regulation of nitric-oxide synthase activity
GO:0070527 platelet aggregation
GO:0090325 regulation of locomotion involved in locomotory behavior
Cellular Component
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005794 Golgi apparatus
GO:0035578 azurophil granule lumen
GO:0043202 lysosomal lumen
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8k7k, PDBe:8k7k, PDBj:8k7k
PDBsum8k7k
PubMed38559739
UniProtP06280|AGAL_HUMAN Alpha-galactosidase A (Gene Name=GLA)

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