Structure of PDB 8ekn Chain B Binding Site BS01

Receptor Information
>8ekn Chain B (length=764) 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
ANPPTLFLVLDNFVERLRKTLSTASVDNPEVGLEYLRRLYPLLRRQFDWF
RKTQAGDIKSYDREAYSTKEAYRWRGRTVSHCLTSGLDDYPRPQPPHPGE
LHVDLMSWVGVMVKSLISIGSLLGATEDVEFYTKVLDAIEHNLDDLHWSE
KEGCYCDATIDEFEEHKLVCHKGYISLFPFLTGLLKPDSPKLGKLLALIG
DESELWSPYGLRSLSKKDEFYGTAENYWRSPVWININYLAIVQLYNIATQ
DGPYKETARDLYTRLRKNIVETVYRNWEETGFAWEQYNPETGKGQRTQHF
TGWTSLVVKIMSGH
Ligand information
Ligand IDWLQ
InChIInChI=1S/C25H30N4O4/c1-16-9-19(21-3-2-8-27-28-21)11-20(10-16)26-12-17-4-6-18(7-5-17)13-29-14-23(31)25(33)24(32)22(29)15-30/h2-11,22-26,30-33H,12-15H2,1H3/t22-,23+,24-,25-/m1/s1
InChIKeySHHWQLKUVLOCSD-ZFFYZDHPSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cc(NCc2ccc(CN3C[CH](O)[CH](O)[CH](O)[CH]3CO)cc2)cc(c1)c4cccnn4
ACDLabs 12.01Cc1cc(cc(c1)NCc1ccc(cc1)CN1CC(O)C(O)C(O)C1CO)c1cccnn1
OpenEye OEToolkits 2.0.7Cc1cc(cc(c1)NCc2ccc(cc2)CN3C[C@@H]([C@H]([C@@H]([C@H]3CO)O)O)O)c4cccnn4
OpenEye OEToolkits 2.0.7Cc1cc(cc(c1)NCc2ccc(cc2)CN3CC(C(C(C3CO)O)O)O)c4cccnn4
CACTVS 3.385Cc1cc(NCc2ccc(CN3C[C@H](O)[C@@H](O)[C@H](O)[C@H]3CO)cc2)cc(c1)c4cccnn4
FormulaC25 H30 N4 O4
Name(2R,3R,4R,5S)-2-(hydroxymethyl)-1-{[4-({[(5P)-3-methyl-5-(pyridazin-3-yl)phenyl]amino}methyl)phenyl]methyl}piperidine-3,4,5-triol
ChEMBL
DrugBank
ZINC
PDB chain8ekn Chain B Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8ekn Structure-Based Design of Potent Iminosugar Inhibitors of Endoplasmic Reticulum alpha-Glucosidase I with Anti-SARS-CoV-2 Activity.
Resolution2.29 Å
Binding residue
(original residue number in PDB)		P412 F417 F421 W423 D424 F475 G584 D586 Y725
Binding residue
(residue number reindexed from 1)		P380 F385 F389 W391 D392 F443 G536 D538 Y677
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8ekn, PDBe:8ekn, PDBj:8ekn
PDBsum8ekn
PubMed36762932
UniProtG0SFD1

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