Structure of PDB 8i5s Chain A Binding Site BS03

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 IDNFG
InChIInChI=1S/C12H13FN2O9/c13-9-11(18)10(17)8(4-16)24-12(9)23-7-2-1-5(14(19)20)3-6(7)15(21)22/h1-3,8-12,16-18H,4H2/t8-,9-,10-,11-,12-/m1/s1
InChIKeyUFSBFVZQJZMIOU-LZQZFOIKSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04[O-][N+](=O)c2ccc(OC1OC(C(O)C(O)C1F)CO)c([N+]([O-])=O)c2
OpenEye OEToolkits 1.5.0c1cc(c(cc1[N+](=O)[O-])[N+](=O)[O-])OC2C(C(C(C(O2)CO)O)O)F
CACTVS 3.341OC[CH]1O[CH](Oc2ccc(cc2[N+]([O-])=O)[N+]([O-])=O)[CH](F)[CH](O)[CH]1O
CACTVS 3.341OC[C@H]1O[C@@H](Oc2ccc(cc2[N+]([O-])=O)[N+]([O-])=O)[C@H](F)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0c1cc(c(cc1[N+](=O)[O-])[N+](=O)[O-])O[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)F
FormulaC12 H13 F N2 O9
Name2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside;
2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucoside;
2,4-dinitrophenyl 2-deoxy-2-fluoro-D-glucoside;
2,4-dinitrophenyl 2-deoxy-2-fluoro-glucoside
ChEMBLCHEMBL1234696
DrugBankDB02658
ZINCZINC000004475142
PDB chain8i5s Chain A Residue 1016 [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)		Q475 D478 T479 L509 W517 I520
Binding residue
(residue number reindexed from 1)		Q443 D446 T447 L477 W485 I488
Annotation score1
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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