Structure of PDB 5abh Chain B Binding Site BS02

Receptor Information
>5abh Chain B (length=669) Species: 818 (Bacteroides thetaiotaomicron) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NVSLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSS
KKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTY
YALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLK
FYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVD
FVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNP
QKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKL
NPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLL
LGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQ
TWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFL
KAFEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQF
KLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQP
GVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMLPLQVKA
NRVLISPVEIELDAIYPGENIQINEISTDGKEWKTVDLKQKESRLSAGLQ
KAPVKFVRFLRQFVLTIEK
Ligand information
Ligand IDYWN
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-/m1/s1
InChIKeyNZYWNYJYZSBEBH-VCDKRKBESA-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-[(2R,3S,4R,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)-1-pentyl-pyrrolidin-2-yl]-N-methyl-ethanamide
ChEMBL
DrugBank
ZINCZINC000263620821
PDB chain5abh Chain B Residue 1717 [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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PDB5abh A Convenient Approach to Stereoisomeric Iminocyclitols: Generation of Potent Brain-Permeable Oga Inhibitors.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		G135 D242 D243 Y282 W286 V314 W337 N339 D344 N372
Binding residue
(residue number reindexed from 1)		G134 D241 D242 Y281 W285 V313 W336 N338 D343 N371
Annotation score1
Binding affinityMOAD: Ki=1.7nM
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:5abh, PDBe:5abh, PDBj:5abh
PDBsum5abh
PubMed26545827
UniProtQ89ZI2|OGA_BACTN O-GlcNAcase BT_4395 (Gene Name=BT_4395)

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