Structure of PDB 5abe Chain A Binding Site BS01

Receptor Information
>5abe Chain A (length=681) Species: 818 (Bacteroides thetaiotaomicron) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VSLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSK
KGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYY
ALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKF
YGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDF
VWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQ
KQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLN
PSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLL
GPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQT
WKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLK
AFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQF
KLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQP
GVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMISNIKNL
PLQVKANRVLISPKWAAGNSVEIELDAIYPGENIQINFLEISTDGKEWKT
VDLKLSAGLQKAPVKFVRFTNLRQFVLTIEK
Ligand information
Ligand IDXQO
InChIInChI=1S/C13H26N2O4/c1-3-4-5-6-15-9(7-11(17)14-2)12(18)13(19)10(15)8-16/h9-10,12-13,16,18-19H,3-8H2,1-2H3,(H,14,17)/t9-,10+,12-,13+/m0/s1
InChIKeyNZYWNYJYZSBEBH-JULQROHOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCN1[C@H](CO)[C@@H](O)[C@@H](O)[C@@H]1CC(=O)NC
OpenEye OEToolkits 1.7.6CCCCCN1C(C(C(C1CO)O)O)CC(=O)NC
OpenEye OEToolkits 1.7.6CCCCCN1[C@H]([C@@H]([C@@H]([C@H]1CO)O)O)CC(=O)NC
CACTVS 3.385CCCCCN1[CH](CO)[CH](O)[CH](O)[CH]1CC(=O)NC
FormulaC13 H26 N2 O4
Name2-[(2S,3S,4R,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)-1-pentyl-pyrrolidin-2-yl]-N-methyl-ethanamide
ChEMBL
DrugBank
ZINCZINC000263620820
PDB chain5abe Chain A Residue 1716 [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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PDB5abe A Convenient Approach to Stereoisomeric Iminocyclitols: Generation of Potent Brain-Permeable Oga Inhibitors.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		Y137 K166 D242 D243 Y282 W337 V342 D344 Y345
Binding residue
(residue number reindexed from 1)		Y135 K164 D240 D241 Y280 W335 V340 D342 Y343
Annotation score1
Binding affinityMOAD: Ki=890uM
PDBbind-CN: -logKd/Ki=3.05,Ki=890uM
Enzymatic activity
Enzyme Commision number 3.2.1.169: protein O-GlcNAcase.
Gene Ontology
Molecular Function
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:0005975 carbohydrate metabolic process
GO:0006517 protein deglycosylation
GO:1901135 carbohydrate derivative metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5abe, PDBe:5abe, PDBj:5abe
PDBsum5abe
PubMed26545827
UniProtQ89ZI2|OGA_BACTN O-GlcNAcase BT_4395 (Gene Name=BT_4395)

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