Structure of PDB 5abg Chain B Binding Site BS02

Receptor Information
>5abg Chain B (length=662) 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
KAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQ
FKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQ
PGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMIKNLPL
QVKANRVLISPVEIELDAIYPGENIQINRLEISDLKQKESSAGLQKAPVK
FVRFQFVLTIEK
Ligand information
Ligand IDV0N
InChIInChI=1S/C17H25FN2O4/c1-19-15(22)9-13-16(23)17(24)14(10-21)20(13)8-2-3-11-4-6-12(18)7-5-11/h4-7,13-14,16-17,21,23-24H,2-3,8-10H2,1H3,(H,19,22)/t13-,14-,16+,17-/m1/s1
InChIKeyIVSNKOONVYNOFH-TXCZRRACSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CNC(=O)C[C@@H]1[C@H](O)[C@H](O)[C@@H](CO)N1CCCc2ccc(F)cc2
OpenEye OEToolkits 1.7.6CNC(=O)CC1C(C(C(N1CCCc2ccc(cc2)F)CO)O)O
OpenEye OEToolkits 1.7.6CNC(=O)C[C@@H]1[C@@H]([C@@H]([C@H](N1CCCc2ccc(cc2)F)CO)O)O
CACTVS 3.385CNC(=O)C[CH]1[CH](O)[CH](O)[CH](CO)N1CCCc2ccc(F)cc2
FormulaC17 H25 F N2 O4
Name2-[(2R,3S,4R,5R)-1-[3-(4-fluorophenyl)propyl]-5-(hydroxymethyl)-3,4-bis(oxidanyl)pyrrolidin-2-yl]-N-methyl-ethanamide
ChEMBL
DrugBank
ZINCZINC000263620578
PDB chain5abg Chain B Residue 1718 [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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PDB5abg A Convenient Approach to Stereoisomeric Iminocyclitols: Generation of Potent Brain-Permeable Oga Inhibitors.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		D242 D243 Y282 W286 V314 W337 N339 D344
Binding residue
(residue number reindexed from 1)		D241 D242 Y281 W285 V313 W336 N338 D343
Annotation score1
Binding affinityMOAD: Ki=9nM
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:5abg, PDBe:5abg, PDBj:5abg
PDBsum5abg
PubMed26545827
UniProtQ89ZI2|OGA_BACTN O-GlcNAcase BT_4395 (Gene Name=BT_4395)

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