Structure of PDB 2w66 Chain B Binding Site BS01

Receptor Information
>2w66 Chain B (length=648) Species: 226186 (Bacteroides thetaiotaomicron VPI-5482) [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
VKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMNLPLQVKA
NRVLISPVEIELDAIYPGENIQINFRLSAGLQKAPVKFVRFFVLTIEK
Ligand information
Ligand IDHQ6
InChIInChI=1S/C9H18N2O5/c1-4(13)11-7-6(14)2-10-5(3-12)8(15)9(7)16/h5-10,12,14-16H,2-3H2,1H3,(H,11,13)/t5-,6-,7+,8-,9-/m1/s1
InChIKeyRJAFVDFBXXHCRJ-SYHAXYEDSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(NC1C(O)C(O)C(NCC1O)CO)C
OpenEye OEToolkits 1.6.1CC(=O)NC1C(CNC(C(C1O)O)CO)O
OpenEye OEToolkits 1.6.1CC(=O)N[C@H]1[C@@H](CN[C@@H]([C@H]([C@@H]1O)O)CO)O
CACTVS 3.352CC(=O)N[CH]1[CH](O)CN[CH](CO)[CH](O)[CH]1O
CACTVS 3.352CC(=O)N[C@H]1[C@H](O)CN[C@H](CO)[C@@H](O)[C@@H]1O
FormulaC9 H18 N2 O5
NameN-[(3R,4S,5R,6R,7R)-3,5,6-trihydroxy-7-(hydroxymethyl)azepan-4-yl]acetamide
ChEMBLCHEMBL541702
DrugBank
ZINCZINC000059124821
PDB chain2w66 Chain B Residue 1716 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2w66 Molecular Basis for Inhibition of Gh84 Glycoside Hydrolases by Substituted Azepanes: Conformational Flexibility Enables Probing of Substrate Distortion.
Resolution2.27 Å
Binding residue
(original residue number in PDB)
G135 K166 D242 D243 Y282 V314 W337 N339 D344
Binding residue
(residue number reindexed from 1)
G132 K163 D239 D240 Y279 V311 W334 N336 D341
Annotation score2
Binding affinityMOAD: Ki=89uM
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

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Molecular Function

View graph for
Biological Process
External links
PDB RCSB:2w66, PDBe:2w66, PDBj:2w66
PDBsum2w66
PubMed19331390
UniProtQ89ZI2|OGA_BACTN O-GlcNAcase BT_4395 (Gene Name=BT_4395)

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