Structure of PDB 2oyk Chain A Binding Site BS01

Receptor Information
>2oyk Chain A (length=434) Species: 1831 (Rhodococcus sp. (in: high G+C Gram-positive bacteria)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PSYLKDDDGRSLILRGFNTASSAKSAPDGMPQFTEADLAREYADMGTNFV
RFLISWRSVEPAPGVYDQQYLDRVEDRVGWYAERGYKVMLDMHQDVYSGA
ITPAIGNGAPAWATYMDGLPVEPQPRWELYYIQPGVMRAFDNFWNTTGKH
PELVEHYAKAWRAVADRFADNDAVVAYDLMNEPFGGSLQGPAFEAGPLAA
MYQRTTDAIRQVDQDTWVCVAPQAIGVNQGLPSGLTKIDDPRAGQQRIAY
CPHLYPLPLHEGLARTLTDVTIDAWRANTAHTARVLGDVPIILGEFGLDT
TLPGARDYIERVYGTAREMGAGVSYWSSDPGPWGPYLPDGTQTLLVDTLN
KPYPRAVAGTPTEWSSTSDRLQLTIEPDAAITAPTEIYLPEAGFPGDVHV
EGADVVGWDRQSRLLTVRTPADSGNVTVTVTPAA
Ligand information
Ligand ID9MR
InChIInChI=1S/C12H23NO8/c14-3-5-1-13-2-6(16)11(5)21-12-10(19)9(18)8(17)7(4-15)20-12/h5-19H,1-4H2/t5-,6-,7-,8-,9+,10-,11-,12+/m1/s1
InChIKeyLEOSSOWHBSKZSO-WUYFHPBOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H]([C@@H](CN1)O)O[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)CO
CACTVS 3.341OC[CH]1CNC[CH](O)[CH]1O[CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O
ACDLabs 10.04O(C1C(O)CNCC1CO)C2OC(C(O)C(O)C2O)CO
OpenEye OEToolkits 1.5.0C1C(C(C(CN1)O)OC2C(C(C(C(O2)CO)O)O)O)CO
CACTVS 3.341OC[C@H]1CNC[C@@H](O)[C@@H]1O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O
FormulaC12 H23 N O8
Name(3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl beta-D-glucopyranoside;
CELLOBIOSE-LIKE ISOFAGOMINE;
(3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl beta-D-glucoside;
(3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl D-glucoside;
(3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl glucoside
ChEMBL
DrugBank
ZINCZINC000016052335
PDB chain2oyk Chain A Residue 600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2oyk The structural basis of glycosidase inhibition by five-membered iminocyclitols: the clan a glycoside hydrolase endoglycoceramidase as a model system.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		K66 H135 D137 W178 E233 Y306 E351 W382
Binding residue
(residue number reindexed from 1)		K24 H93 D95 W127 E182 Y255 E295 W326
Annotation score1
Binding affinityMOAD: Ki=5uM
PDBbind-CN: -logKd/Ki=5.30,Ki=5uM
Enzymatic activity
Enzyme Commision number 3.2.1.123: endoglycosylceramidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0047876 endoglycosylceramidase activity
Biological Process
GO:0000272 polysaccharide catabolic process
GO:0005975 carbohydrate metabolic process
GO:0016042 lipid catabolic process
GO:1901136 carbohydrate derivative catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2oyk, PDBe:2oyk, PDBj:2oyk
PDBsum2oyk
PubMed17487923
UniProtO33853

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