Structure of PDB 8e5u Chain B Binding Site BS01

Receptor Information
>8e5u Chain B (length=763) Species: 759272 (Thermochaetoides thermophila DSM 1495) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SILHSEIGRLNNQSLLWGPYRPNIYFGTRPRIGKSLMTGLMWGKIESYTD
FQHTVRYTCEQNEGMKGYGWDEYDPRRGGIQSIHDIQNGLDITTSFVKIP
GGAHGGSWAARIKGTLNDDAPKDQKTIVVFYVSQEGENSELEAVPSENEF
GYEGDVILKGRSEALGNYKLVVTKGKGVIPQSDHDLSRLRGPGQTVVQSL
TYPDEVLWQAKPILFQQLKAGIDWLVENKYDVADPPPPWQVYLLANKPGS
GNVHIVQKVFEGDFEFDILFSSESAGKEVTSKDLEREVKQATEVFGERFA
RVFDLKAPFQGDNYKKFGKSMFSNLIGGIGYFYGHSLVDRSYAPEYDEEN
EGFWEDAAEARARHQEALEGPYELFTSIPSRPFFPRGFLWDEGFHLLPIA
DWDIDLALEIIKSWYNLMDEDGWIAREQILGAEARSKVPKEFQTQYPHYA
NPPTLFLVLDNFVERLRKTLSTASVDNPEVGLEYLRRLYPLLRRQFDWFR
KTQAGDIKSYDREAYSTKEAYRWRGRTVSHCLTSGLDDYPRPQPPHPGEL
HVDLMSWVGVMVKSLISIGSLLGATEDVEFYTKVLDAIEHNLDDLHWSEK
EGCYCDATIDEFEEHKLVCHKGYISLFPFLTGLLKPDSPKLGKLLALIGD
ESELWSPYGLRSLSKKDEFYGTAENYWRSPVWININYLAIVQLYNIATQD
GPYKETARDLYTRLRKNIVETVYRNWEETGFAWEQYNPETGKGQRTQHFT
GWTSLVVKIMSGH
Ligand information
Ligand IDUPH
InChIInChI=1S/C24H38N4O7/c29-13-21-23(31)24(32)22(30)12-26(21)10-4-2-1-3-9-25-19-8-7-16(11-20(19)28(33)34)27-17-5-6-18(27)15-35-14-17/h7-8,11,17-18,21-25,29-32H,1-6,9-10,12-15H2/t17-,18+,21-,22+,23-,24-/m1/s1
InChIKeyQGCBQROIBSZCHP-OAOHXRHQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cc(c(cc1N2[C@@H]3CC[C@H]2COC3)[N+](=O)[O-])NCCCCCCN4C[C@@H]([C@H]([C@@H]([C@H]4CO)O)O)O
CACTVS 3.385OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](O)CN1CCCCCCNc2ccc(cc2[N+]([O-])=O)N3[C@H]4CC[C@@H]3COC4
CACTVS 3.385OC[CH]1[CH](O)[CH](O)[CH](O)CN1CCCCCCNc2ccc(cc2[N+]([O-])=O)N3[CH]4CC[CH]3COC4
ACDLabs 12.01OCC1C(O)C(O)C(O)CN1CCCCCCNc1ccc(cc1[N+]([O-])=O)N1C2CCC1COC2
OpenEye OEToolkits 2.0.7c1cc(c(cc1N2C3CCC2COC3)[N+](=O)[O-])NCCCCCCN4CC(C(C(C4CO)O)O)O
FormulaC24 H38 N4 O7
Name(2R,3R,4R,5S)-2-(hydroxymethyl)-1-(6-{2-nitro-4-[(1R,5S)-3-oxa-8-azabicyclo[3.2.1]octan-8-yl]anilino}hexyl)piperidine-3,4,5-triol
ChEMBL
DrugBank
ZINC
PDB chain8e5u Chain B Residue 1003 [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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PDB8e5u Structure-Based Design of Potent Iminosugar Inhibitors of Endoplasmic Reticulum alpha-Glucosidase I with Anti-SARS-CoV-2 Activity.
Resolution2.33 Å
Binding residue
(original residue number in PDB)		F417 R419 F421 W423 D424 F475 G584 D586 Y725 F798
Binding residue
(residue number reindexed from 1)		F384 R386 F388 W390 D391 F442 G535 D537 Y676 F749
Annotation score1
Enzymatic activity
Enzyme Commision number 3.2.1.106: mannosyl-oligosaccharide glucosidase.
Gene Ontology
Molecular Function
GO:0004573 Glc3Man9GlcNAc2 oligosaccharide glucosidase activity
GO:0016787 hydrolase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006487 protein N-linked glycosylation
GO:0009311 oligosaccharide metabolic process
Cellular Component
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8e5u, PDBe:8e5u, PDBj:8e5u
PDBsum8e5u
PubMed36762932
UniProtG0SFD1

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