Structure of PDB 3s5y Chain B Binding Site BS02

Receptor Information
>3s5y Chain B (length=391) 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
CFITQLLPVKRKLGFYEWTSRLRSHINPTGTVLLQLENTMQ
Ligand information
Ligand IDDGJ
InChIInChI=1S/C6H13NO4/c8-2-3-5(10)6(11)4(9)1-7-3/h3-11H,1-2H2/t3-,4+,5+,6-/m1/s1
InChIKeyLXBIFEVIBLOUGU-DPYQTVNSSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01OC1C(NCC(O)C1O)CO
OpenEye OEToolkits 1.7.2C1C(C(C(C(N1)CO)O)O)O
OpenEye OEToolkits 1.7.2C1[C@@H]([C@H]([C@H]([C@H](N1)CO)O)O)O
CACTVS 3.370OC[CH]1NC[CH](O)[CH](O)[CH]1O
CACTVS 3.370OC[C@H]1NC[C@H](O)[C@@H](O)[C@H]1O
FormulaC6 H13 N O4
Name(2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol;
1-deoxygalactonojirimycin
ChEMBLCHEMBL110458
DrugBankDB05018
ZINCZINC000001636704
PDB chain3s5y Chain B Residue 802 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3s5y The molecular basis of pharmacological chaperoning in human alpha-galactosidase
Resolution2.105 Å
Binding residue
(original residue number in PDB)		W47 D92 D93 C142 K168 D170 E203 R227 D231
Binding residue
(residue number reindexed from 1)		W16 D61 D62 C111 K137 D139 E172 R196 D200
Annotation score1
Binding affinityMOAD: Ki=39nM
PDBbind-CN: -logKd/Ki=7.41,Ki=39.1nM
BindingDB: IC50=70nM
Enzymatic activity
Catalytic site (original residue number in PDB) D170 D231
Catalytic site (residue number reindexed from 1) D139 D200
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3s5y, PDBe:3s5y, PDBj:3s5y
PDBsum3s5y
PubMed22195554
UniProtP06280|AGAL_HUMAN Alpha-galactosidase A (Gene Name=GLA)

[Back to BioLiP]