Structure of PDB 5m7t Chain A Binding Site BS01

Receptor Information
>5m7t Chain A (length=451) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RFLCGVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWR
EMYSVEEAEQLMTLISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKL
DQVSQFGCRSFALLFDDIDHNMCAADKEVFSSFAHAQVSITNEIYQYLGE
PETFLFCPTEYCGTFCYPNVSQSPYLRTVGEKLLPGIEVLWTGPKVVSKE
IPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLFLGPYKGRSTELIPRLK
GVLTNPNCEFEANYVAIHTLATWYKSNMNDVLYSPQMALKLALTEWLQEF
GVPHQFVPGPNEKPLYTAEPVTLEDLQLLADLFYLPYEHGPKGAQMLREF
QWLRANSSVVSVKDSEKIEEWRSRAAKFEEMCGLVMGMFTRLSNCANRTI
LYDMYSYVWDIKSIMSMVKSFVQWLGCRSHSQEPWAFRGGLAGEFQRLLP
I
Ligand information
Ligand IDGDV
InChIInChI=1S/C17H20N4O5/c1-9(23)18-13-15(25)14(24)12(8-22)21-7-11(20-16(13)21)17(26)19-10-5-3-2-4-6-10/h2-7,12-15,22,24-25H,8H2,1H3,(H2,18,19,23,26)/p+1/t12-,13-,14-,15-/m1/s1
InChIKeyWWSQBPPKQTUEDT-KBUPBQIOSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=O)N[C@H]1c2[nH]c(c[n+]2[C@@H]([C@H]([C@@H]1O)O)CO)C(=O)Nc3ccccc3
CACTVS 3.341CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)[n+]2cc([nH]c12)C(=O)Nc3ccccc3
OpenEye OEToolkits 1.5.0CC(=O)NC1c2[nH]c(c[n+]2C(C(C1O)O)CO)C(=O)Nc3ccccc3
CACTVS 3.341CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)[n+]2cc([nH]c12)C(=O)Nc3ccccc3
ACDLabs 10.04O=C(c1c[n+]2c(n1)C(NC(=O)C)C(O)C(O)C2CO)Nc3ccccc3
FormulaC17 H21 N4 O5
Name(5R,6R,7R,8S)-8-(ACETYLAMINO)-6,7-DIHYDROXY-5-(HYDROXYMETHYL)-N-PHENYL-1,5,6,7,8,8A-HEXAHYDROIMIDAZO[1,2-A]PYRIDINE-2-CARBOXAMIDE
ChEMBL
DrugBank
ZINCZINC000103542861
PDB chain5m7t Chain A Residue 1001 [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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PDB5m7t Structural and functional insight into human O-GlcNAcase.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		G67 K98 D175 Y219 F223 V254 W278 N280 D285
Binding residue
(residue number reindexed from 1)		G9 K40 D117 Y161 F165 V196 W220 N222 D227
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.41,Ki=3.9uM
Enzymatic activity
Enzyme Commision number 3.2.1.169: protein O-GlcNAcase.
Gene Ontology
Molecular Function
GO:0004415 hyalurononglucosaminidase activity
GO:0015929 hexosaminidase activity
GO:0016231 beta-N-acetylglucosaminidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0042802 identical protein binding
GO:0102571 [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity
Biological Process
GO:0006044 N-acetylglucosamine metabolic process
GO:0006493 protein O-linked glycosylation
GO:0006516 glycoprotein catabolic process
GO:0006517 protein deglycosylation
GO:0009100 glycoprotein metabolic process
GO:1901135 carbohydrate derivative metabolic process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5m7t, PDBe:5m7t, PDBj:5m7t
PDBsum5m7t
PubMed28346405
UniProtO60502|OGA_HUMAN Protein O-GlcNAcase (Gene Name=OGA)

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