Structure of PDB 4do5 Chain A Binding Site BS01

Receptor Information
>4do5 Chain A (length=387) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LDNGLLQTPPMGWLAWERFRCNINCDEDPKNCISEQLFMEMADRMAQDGW
RDMGYTYLNIDDCWIGGRDASGRLMPDPKRFPHGIPFLADYVHSLGLKLG
IYADMGNFTCMGYPGTTLDKVVQDAQTFAEWKVDMLKLDGCFSTPEERAQ
GYPKMAAALNATGRPIAFSCSWPAYEGGLPPRVQYSLLADICNLWRNYDD
IQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSR
AQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRI
HKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYE
AQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIK
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 chain4do5 Chain A Residue 509 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4do5 Pharmacological chaperones for human alpha-N-acetylgalactosaminidase
Resolution1.51 Å
Binding residue
(original residue number in PDB)		W33 D78 D79 C127 K154 D156 R213 D217
Binding residue
(residue number reindexed from 1)		W16 D61 D62 C110 K137 D139 R196 D200
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.83,Ki=1.48uM
Enzymatic activity
Catalytic site (original residue number in PDB) D156 D217
Catalytic site (residue number reindexed from 1) D139 D200
Enzyme Commision number 3.2.1.49: alpha-N-acetylgalactosaminidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004557 alpha-galactosidase activity
GO:0008456 alpha-N-acetylgalactosaminidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0042803 protein homodimerization activity
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006629 lipid metabolic process
GO:0009311 oligosaccharide metabolic process
GO:0016052 carbohydrate catabolic process
GO:0016139 glycoside catabolic process
GO:0019377 glycolipid catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005764 lysosome
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:4do5, PDBe:4do5, PDBj:4do5
PDBsum4do5
PubMed23045655
UniProtP17050|NAGAB_HUMAN Alpha-N-acetylgalactosaminidase (Gene Name=NAGA)

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