Structure of PDB 8i5s Chain A Binding Site BS01

Receptor Information
>8i5s Chain A (length=769) Species: 858215 (Thermoanaerobacterium xylanolyticum LX-11) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKISHKIDIPDSAWTIGIGEKFKNAGHPNVKYPMIDDSYVQGAPLGGFGA
GTIGRTYNGGFSRWHLEIGKNKYTTVYANQFSVFQKVEGNKDGVAQVLYA
GEPENGYLSSWKWDYPKESGMYYALYPNSWYTYTNKDLPVQLAVKQFSPI
IPYNYKETSYPVAVFKWTAYNPTNKNVDVSIMFTWQNMIGFFGKQVNVNS
GNFNKIIKDKSKDSEIVAAVMGNISNDNEEWNGEYSIGVKKVPGVDISYK
AKFVTTGDGSDLWHEFSKNGILDNKDDETPTKQDGIGSAIAVNFKLQPGQ
TIEVPFALSWDLPIMKFGGGDKWYKMYTKYFGKNGKNSFAILKEALNNYQ
KWEKMIDDWQKPILSNKSKPDWYKTALFNELYYLADGGTAWENGKVGEKR
TNNMFGLLECFDYNYYETLDVRFYGSFPLVMLWPDIEKQVMRQFADTINV
QDSSEFKVGSNGAMAVKKVQGMIPHDLGSSYALPWIKINAYDWQNPNIWK
DLNSKYVLLVYRDYVLTGKTDKEFLKYTWKSVKTALDKLKEMDKDNDGIP
DNEGIPDQTYNTWSMKGTSAYCGSLWLAALKAAQEIGKVLKDNEAYIKYN
EWYKIAQQNFEKELWNGEYYNFDTESDHKDSIMADQLAGQWYADILRLGD
ILPKDHVQKALKKIYEFNVMKFENGKMGAVNGMRPDGIVDESDIQAQEVW
TGVTYALASFMKYRGMTEEAYNTAYGVYKMTYDKSGKGYWFRTPEAWTKD
GNYRASMYMRPLSIWSMEV
Ligand information
Ligand IDG2F
InChIInChI=1S/C6H11FO5/c7-3-5(10)4(9)2(1-8)12-6(3)11/h2-6,8-11H,1H2/t2-,3-,4-,5-,6+/m1/s1
InChIKeyZCXUVYAZINUVJD-UKFBFLRUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C(C1C(C(C(C(O1)O)F)O)O)O
CACTVS 3.370OC[CH]1O[CH](O)[CH](F)[CH](O)[CH]1O
OpenEye OEToolkits 1.7.0C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)F)O)O)O
CACTVS 3.370OC[C@H]1O[C@H](O)[C@H](F)[C@@H](O)[C@@H]1O
ACDLabs 12.01FC1C(O)C(O)C(OC1O)CO
FormulaC6 H11 F O5
Name2-deoxy-2-fluoro-alpha-D-glucopyranose;
2-deoxy-2-fluoro-alpha-D-glucose;
2-deoxy-2-fluoro-D-glucose;
2-deoxy-2-fluoro-glucose
ChEMBLCHEMBL1086863
DrugBankDB04282
ZINCZINC000003809846
PDB chain8i5s Chain A Residue 1000 [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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PDB8i5s Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation.
Resolution1.45 Å
Binding residue
(original residue number in PDB)		E441 Y445 D452 H507 T591 E777 R786
Binding residue
(residue number reindexed from 1)		E409 Y413 D420 H475 T559 E745 R754
Annotation score3
Enzymatic activity
Enzyme Commision number 3.2.1.45: glucosylceramidase.
Gene Ontology
Molecular Function
GO:0004348 glucosylceramidase activity
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0008422 beta-glucosidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0046872 metal ion binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006680 glucosylceramide catabolic process
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8i5s, PDBe:8i5s, PDBj:8i5s
PDBsum8i5s
PubMed37180965
UniProtF6BL85

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