Structure of PDB 8eud Chain B Binding Site BS01

Receptor Information
>8eud Chain B (length=767) Species: 759272 (Thermochaetoides thermophila DSM 1495) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ESILHSEIGRLNNQSLLWGPYRPNIYFGTRPRIGKSLMTGLMWGKIESYT
DFQHTVRYTCEQNEGMKGYGWDEYDPRRGGIQSIHDIQNGLDITTSFVKI
PGGAHGGSWAARIKGTLNDDAPKDQKTIVVFYVSQEGENSELEAVPSENE
FGYEGDVILKGRSEALGNYKLVVTKGKGVIPQSDHDLSRLRGPGQTVVQS
LTYPDEVLWQAKPILFQQLKAGIDWLVENKYDVADPPPPWQVYLLANKPG
SGNVHIVQKVFEGDFEFDILFSSESAGKEVTSKDLEREVKQATEVFGERF
ARVFDLKAPFQGDNYKKFGKSMFSNLIGGIGYFYGHSLVDRSYAPEYDEE
NEGFWEDAAEARARHQEALEGPYELFTSIPSRPFFPRGFLWDEGFHLLPI
ADWDIDLALEIIKSWYNLMDEDGWIAREQILGAEARSKVPKEFQTQYPHY
ANPPTLFLVLDNFVERLRKNNATLSTASVDNPEVGLEYLRRLYPLLRRQF
DWFRKTQAGDIKSYDREAYSTKEAYRWRGRTVSHCLTSGLDDYPRPQPPH
PGELHVDLMSWVGVMVKSLISIGSLLGATEDVEFYTKVLDAIEHNLDDLH
WSEKEGCYCDATIDEFEEHKLVCHKGYISLFPFLTGLLKPDSPKLGKLLA
LIGDESELWSPYGLRSLSKKDEFYGTAENYWRSPVWININYLAIVQLYNI
ATQDGPYKETARDLYTRLRKNIVETVYRNWEETGFAWEQYNPETGKGQRT
QHFTGWTSLVVKIMSGH
Ligand information
Ligand IDWUR
InChIInChI=1S/C24H33N5O4/c1-16-27-18-13-17(24-25-9-6-10-26-24)7-8-19(18)29(16)12-5-3-2-4-11-28-14-21(31)23(33)22(32)20(28)15-30/h6-10,13,20-23,30-33H,2-5,11-12,14-15H2,1H3/t20-,21+,22-,23-/m1/s1
InChIKeyXPRZPIFSIBBCSM-KAOXLYBCSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01Cc1nc2cc(ccc2n1CCCCCCN1CC(O)C(O)C(O)C1CO)c1ncccn1
CACTVS 3.385Cc1nc2cc(ccc2n1CCCCCCN3C[C@H](O)[C@@H](O)[C@H](O)[C@H]3CO)c4ncccn4
OpenEye OEToolkits 2.0.7Cc1nc2cc(ccc2n1CCCCCCN3CC(C(C(C3CO)O)O)O)c4ncccn4
OpenEye OEToolkits 2.0.7Cc1nc2cc(ccc2n1CCCCCCN3C[C@@H]([C@H]([C@@H]([C@H]3CO)O)O)O)c4ncccn4
CACTVS 3.385Cc1nc2cc(ccc2n1CCCCCCN3C[CH](O)[CH](O)[CH](O)[CH]3CO)c4ncccn4
FormulaC24 H33 N5 O4
Name(2R,3R,4R,5S)-2-(hydroxymethyl)-1-{6-[2-methyl-5-(pyrimidin-2-yl)-1H-benzimidazol-1-yl]hexyl}piperidine-3,4,5-triol
ChEMBL
DrugBank
ZINC
PDB chain8eud Chain B Residue 1005 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8eud Structure-Based Design of Potent Iminosugar Inhibitors of Endoplasmic Reticulum alpha-Glucosidase I with Anti-SARS-CoV-2 Activity.
Resolution2.37 Å
Binding residue
(original residue number in PDB)		P412 F421 W423 D424 F475 G584 D586 Y725
Binding residue
(residue number reindexed from 1)		P380 F389 W391 D392 F443 G539 D541 Y680
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8eud, PDBe:8eud, PDBj:8eud
PDBsum8eud
PubMed36762932
UniProtG0SFD1

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