Structure of PDB 5npf Chain A Binding Site BS02

Receptor Information
>5npf Chain A (length=763) Species: 29329 (Thermoanaerobacterium xylanolyticum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKISHKIDIPDSAWTIGIGEKFKNAGHPNVKYPMIDDSYVQGAPLGGFGA
GTIGRTYNGGFSRWHLEIGKNKYTTVYANQFSVFQKVEGNKDGVAQVLYA
GEPGYLSSWKWDYPKESGMYYALYPNSWYTYTNKDLPVQLAVKQFSPIIP
YNYKETSYPVAVFKWTAYNPTNKNVDVSIMFTWQNMIGFFGKQVNVNSGN
FNKIIKDKSEIVAAVMGNISNDNEEWNGEYSIGVKKVPGVDISYKAKFVT
TGDGSDLWHEFSKNGILDNKDDETPTKQDGIGSAIAVNFKLQPGQTIEVP
FALSWDLPIMKFGGGDKWYKMYTKYFGKNGKNSFAILKEALNNYQKWEKM
IDDWQKPILSNKSKPDWYKTALFNELYYLADGGTAWENGKVGERTNNMFG
LLECFDYNYYETLDVRFYGSFPLVMLWPDIEKQVMRQFADTINVQDSSEF
KVGSNGAMAVKKVQGMIPHDLGSSYALPWIKINAYDWQNPNIWKDLNSKY
VLLVYRDYVLTGKTDKEFLKYTWKSVKTALDKLKEMDKDNDGIPDNEGIP
DQTYDTWSMKGTSAYCGSLWLAALKAAQEIGKVLKDNEAYIKYNEWYKIA
QQNFEKELWNGEYYNFDTESDHKDSIMADQLAGQWYADILRLGDILPKDH
VQKALKKIYEFNVMKFENGKMGAVNGMRPDGIVDESDIQAQEVWTGVTYA
LASFMKYRGMTEEAYNTAYGVYKMTYDKSGKGYWFRTPEAWTKDGNYRAS
MYMRPLSIWSMEV
Ligand information
Ligand ID945
InChIInChI=1S/C7H14O9S/c8-1-2-3(9)4(10)5(11)6(12)7(2)16-17(13,14)15/h2-12H,1H2,(H,13,14,15)/t2-,3-,4+,5-,6+,7-/m1/s1
InChIKeyPDBNIRCVRHFXAD-XQCVOTFFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C(C1C(C(C(C(C1OS(=O)(=O)O)O)O)O)O)O
CACTVS 3.385OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H]1O[S](O)(=O)=O
OpenEye OEToolkits 2.0.6C([C@@H]1[C@H]([C@@H]([C@H](C([C@@H]1OS(=O)(=O)O)O)O)O)O)O
CACTVS 3.385OC[CH]1[CH](O)[CH](O)[CH](O)[CH](O)[CH]1O[S](O)(=O)=O
FormulaC7 H14 O9 S
Name[(1~{R},2~{R},3~{R},4~{S},5~{R})-2-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl)cyclohexyl] hydrogen sulfate
ChEMBL
DrugBank
ZINC
PDB chain5npf Chain A Residue 915 [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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PDB5npf 1,6-Cyclophellitol Cyclosulfates: A New Class of Irreversible Glycosidase Inhibitor.
Resolution1.38 Å
Binding residue
(original residue number in PDB)		E441 Y445 D452 H507 Y523 T591 D593 E777 R786
Binding residue
(residue number reindexed from 1)		E403 Y407 D414 H469 Y485 T553 D555 E739 R748
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.24,IC50=58uM
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:5npf, PDBe:5npf, PDBj:5npf
PDBsum5npf
PubMed28776021
UniProtF6BL85

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