Structure of PDB 3rx8 Chain A Binding Site BS04

Receptor Information
>3rx8 Chain A (length=528) Species: 1388 (Alicyclobacillus acidocaldarius subsp. acidocaldarius) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KSIFYNQVGYLISGDKRFWIQAHEPQPFALRTPEGQAVFAGMTKPVGGNW
YVGDFTALRVPGTYTLTVGTLEARVVIHRRAYRDVLEAMLRFFDYQLCGV
VLPEDEAGPWAHGACHTSDAKVFGTERALACPGGWHDAGDYGKYTVPAAK
AVADLLLAHEYFPAALAHVRPMRSVHRAPHLPPALEVAREEIAWLLTMQD
PATGGVYHKVTTPSFPPLDTRPEDDDAPLVLSPISYAATATFCAAMAHAA
LVYRPFDPALSSCCADAARRAYAWLGAHEMQPFHNPDGILTGEYGDAELR
DELLWASCALLRMTGDSAWARVCEPLLDLDLPWELGWADVALYGVMDYLR
TPRAAVSDDVRNKVKSRLLRELDALAAMAESHPFGIPMRDDDFIWGSNMV
LLNRAMAFLLAEGVGVLHPAAHTVAQRAADYLFGANPLGQCYVTGFGQRP
VRHPHHRPSVADDVDHPVPGMVVGGPNRHLQDEIARAQLAGRPAMEAYID
HQDSYSTNEVAVYWNSPAVFVIAALLEA
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 chain3rx8 Chain A Residue 601 [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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PDB3rx8 Fortuitious binding of inhibitors-derived isofagomine for inverting GH9 beta-glycosidases
Resolution2.56 Å
Binding residue
(original residue number in PDB)
D143 D146 G298 Y300 W343 W401 E515 Y519
Binding residue
(residue number reindexed from 1)
D137 D140 G292 Y294 W337 W395 E509 Y513
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.21,Ki=610nM
Enzymatic activity
Catalytic site (original residue number in PDB) D143 D146 Y300 E515
Catalytic site (residue number reindexed from 1) D137 D140 Y294 E509
Enzyme Commision number 3.2.1.4: cellulase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0008810 cellulase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0046872 metal ion binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0030245 cellulose catabolic process

View graph for
Molecular Function

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Biological Process
External links
PDB RCSB:3rx8, PDBe:3rx8, PDBj:3rx8
PDBsum3rx8
PubMed21785782
UniProtQ9AJS0

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