Structure of PDB 5nn6 Chain A Binding Site BS01

Receptor Information
>5nn6 Chain A (length=845) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QCDVPPNSRFDCAPDKAITQEQCEARGCCYIPAKQGQPWCFFPPSYPSYK
LENLSSSEMGYTATLTRTTPTFFPKDILTLRLDVMMETENRLHFTIKDPA
NRRYEVPLAPSPLYSVEFSEEPFGVIVHRQLDGRVLLNTTVAPLFFADQF
LQLSTSLPSQYITGLAEHLSPLMLSTSWTRITLWNRDLAPTPGANLYGSH
PFYLALEDGGSAHGVFLLNSNAMDVVLQPSPALSWRSTGGILDVYIFLGP
EPKSVVQQYLDVVGYPFMPPYWGLGFHLCRWGYSSTAITRQVVENMTRAH
FPLDVQWNDLDYMDSRRDFTFNKDGFRDFPAMVQELHQGGRRYMMIVDPA
ISSSGPAGSYRPYDEGLRRGVFITNETGQPLIGKVWPGSTAFPDFTNPTA
LAWWEDMVAEFHDQVPFDGMWIDMNEPSNFIRGSEDGCPNNELENPPYVP
GVVGGTLQAATICASSHQFLSTHYNLHNLYGLTEAIASHRALVKARGTRP
FVISRSTFAGHGRYAGHWTGDVWSSWEQLASSVPEILQFNLLGVPLVGAD
VCGFLGNTSEELCVRWTQLGAFYPFMRNHNSLLSLPQEPYSFSEPAQQAM
RKALTLRYALLPHLYTLFHQAHVAGETVARPLFLEFPKDSSTWTVDHQLL
WGEALLITPVLQAGKAEVTGYFPLGTWYDLQTVPIEREPAIHSEGQWVTL
PAPLDTINVHLRAGYIIPLQGPGLTTTESRQQPMALAVALTKGGEARGEL
FWDDGESLEVLERGAYTQVIFLARNNTIVNELVRVTSEGAGLQLQKVTVL
GVATAPQQVLSNGVPVSNFTYSPDTKVLDICVSLLMGEQFLVSWC
Ligand information
Ligand IDMIG
InChIInChI=1S/C8H17NO5/c10-2-1-9-3-6(12)8(14)7(13)5(9)4-11/h5-8,10-14H,1-4H2/t5-,6+,7-,8-/m1/s1
InChIKeyIBAQFPQHRJAVAV-ULAWRXDQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1[C@@H]([C@H]([C@@H]([C@H]([N@@]1CCO)CO)O)O)O
OpenEye OEToolkits 1.7.0C1C(C(C(C(N1CCO)CO)O)O)O
CACTVS 3.352OCCN1C[CH](O)[CH](O)[CH](O)[CH]1CO
CACTVS 3.352OCCN1C[C@H](O)[C@@H](O)[C@H](O)[C@H]1CO
FormulaC8 H17 N O5
Name(2R,3R,4R,5S)-1-(2-hydroxyethyl)-2-(hydroxymethyl)piperidine-3,4,5-triol;
Miglitol
ChEMBLCHEMBL1561
DrugBankDB00491
ZINCZINC000004097426
PDB chain5nn6 Chain A Residue 1013 [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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PDB5nn6 Structure of human lysosomal acid alpha-glucosidase-a guide for the treatment of Pompe disease.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		W376 D404 L405 W481 D518 M519 R600 W613 D616 F649 H674
Binding residue
(residue number reindexed from 1)		W281 D309 L310 W386 D423 M424 R505 W518 D521 F554 H579
Annotation score1
Binding affinityMOAD: Ki=3uM
PDBbind-CN: -logKd/Ki=5.52,Kd=3.0uM
BindingDB: IC50=2000nM
Enzymatic activity
Enzyme Commision number 3.2.1.20: alpha-glucosidase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004558 alpha-1,4-glucosidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0030246 carbohydrate binding
GO:0090599 alpha-glucosidase activity
Biological Process
GO:0000023 maltose metabolic process
GO:0002026 regulation of the force of heart contraction
GO:0002086 diaphragm contraction
GO:0003007 heart morphogenesis
GO:0005975 carbohydrate metabolic process
GO:0005977 glycogen metabolic process
GO:0005980 glycogen catabolic process
GO:0005985 sucrose metabolic process
GO:0006006 glucose metabolic process
GO:0006941 striated muscle contraction
GO:0007040 lysosome organization
GO:0007626 locomotory behavior
GO:0009888 tissue development
GO:0035904 aorta development
GO:0043181 vacuolar sequestering
GO:0046716 muscle cell cellular homeostasis
GO:0050884 neuromuscular process controlling posture
GO:0050885 neuromuscular process controlling balance
GO:0060048 cardiac muscle contraction
GO:0061723 glycophagy
Cellular Component
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0035577 azurophil granule membrane
GO:0043202 lysosomal lumen
GO:0043231 intracellular membrane-bounded organelle
GO:0070062 extracellular exosome
GO:0070821 tertiary granule membrane
GO:0101003 ficolin-1-rich granule membrane
GO:0120282 autolysosome lumen

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5nn6, PDBe:5nn6, PDBj:5nn6
PDBsum5nn6
PubMed29061980
UniProtP10253|LYAG_HUMAN Lysosomal alpha-glucosidase (Gene Name=GAA)

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