Structure of PDB 5abf Chain A Binding Site BS01

Receptor Information
>5abf Chain A (length=663) Species: 818 (Bacteroides thetaiotaomicron) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKK
GMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYA
LQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFY
GKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFV
WAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQK
QAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNP
SIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLG
PVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTW
KDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKA
FKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFK
LTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPG
VKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMISNNLPLQ
VKANRVLISVEIELDAIYPGENIQIGRLEISTDGKEWKTVDLKSAGLQKA
PVKFVRFVLTIEK
Ligand information
Ligand IDXRJ
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-XKAARJIMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCCCCN1[C@H]([C@H]([C@@H]([C@H]1CO)O)O)CC(=O)NC
OpenEye OEToolkits 1.7.6CCCCCN1C(C(C(C1CO)O)O)CC(=O)NC
CACTVS 3.385CCCCCN1[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1CC(=O)NC
CACTVS 3.385CCCCCN1[CH](CO)[CH](O)[CH](O)[CH]1CC(=O)NC
FormulaC13 H26 N2 O4
Name2-[(2S,3R,4R,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)-1-pentyl-pyrrolidin-2-yl]-N-methyl-ethanamide
ChEMBL
DrugBank
ZINCZINC000263620822
PDB chain5abf Chain A Residue 1717 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5abf A Convenient Approach to Stereoisomeric Iminocyclitols: Generation of Potent Brain-Permeable Oga Inhibitors.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		G135 Y137 K166 D242 D243 Y282 W286 T310 W337 D344 Y345
Binding residue
(residue number reindexed from 1)		G132 Y134 K163 D239 D240 Y279 W283 T307 W334 D341 Y342
Annotation score1
Binding affinityMOAD: Ki=14uM
PDBbind-CN: -logKd/Ki=4.85,Ki=14uM
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:5abf, PDBe:5abf, PDBj:5abf
PDBsum5abf
PubMed26545827
UniProtQ89ZI2|OGA_BACTN O-GlcNAcase BT_4395 (Gene Name=BT_4395)

[Back to BioLiP]