Structure of PDB 2w67 Chain A Binding Site BS01

Receptor Information
>2w67 Chain A (length=642) Species: 226186 (Bacteroides thetaiotaomicron VPI-5482) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSKGML
ISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQT
FAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKN
KMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAI
HPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAE
LLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQ
IMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVY
GNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDA
IRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKE
GKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTA
EMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKT
ATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMNLPLQVKANRV
LISPVEIELDAIYPGENIQINFGLQKAPVKFVRFQFVLTIEK
Ligand information
Ligand IDF34
InChIInChI=1S/C8H16N2O4/c1-4(11)10-5-2-9-3-6(12)8(14)7(5)13/h5-9,12-14H,2-3H2,1H3,(H,10,11)/t5-,6+,7+,8+/m0/s1
InChIKeyRGHXJBVAPJFIEQ-LXGUWJNJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1CC(=O)N[C@H]1CNC[C@H]([C@H]([C@@H]1O)O)O
ACDLabs 10.04O=C(NC1CNCC(O)C(O)C1O)C
CACTVS 3.352CC(=O)N[C@H]1CNC[C@@H](O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.6.1CC(=O)NC1CNCC(C(C1O)O)O
CACTVS 3.352CC(=O)N[CH]1CNC[CH](O)[CH](O)[CH]1O
FormulaC8 H16 N2 O4
NameN-[(3S,4R,5R,6R)-4,5,6-trihydroxyazepan-3-yl]acetamide
ChEMBL
DrugBank
ZINC
PDB chain2w67 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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PDB2w67 Molecular Basis for Inhibition of Gh84 Glycoside Hydrolases by Substituted Azepanes: Conformational Flexibility Enables Probing of Substrate Distortion.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		K166 D242 D243 Y282 V314 W337 N339 D344
Binding residue
(residue number reindexed from 1)		K160 D236 D237 Y276 V308 W331 N333 D338
Annotation score1
Binding affinityMOAD: Ki=11uM
PDBbind-CN: -logKd/Ki=4.96,Ki=11uM
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:2w67, PDBe:2w67, PDBj:2w67
PDBsum2w67
PubMed19331390
UniProtQ89ZI2|OGA_BACTN O-GlcNAcase BT_4395 (Gene Name=BT_4395)

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