Structure of PDB 8ecw Chain B Binding Site BS01

Receptor Information
>8ecw 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 IDX5B
InChIInChI=1S/C26H31ClN4O4/c27-20-12-19(22-2-1-9-29-30-22)13-21(14-20)28-10-7-17-3-5-18(6-4-17)8-11-31-15-24(33)26(35)25(34)23(31)16-32/h1-6,9,12-14,23-26,28,32-35H,7-8,10-11,15-16H2/t23-,24+,25-,26-/m1/s1
InChIKeyOCKWGRBGNLPCDQ-XDZVQPMWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cc(nnc1)c2cc(cc(c2)Cl)NCCc3ccc(cc3)CCN4CC(C(C(C4CO)O)O)O
OpenEye OEToolkits 2.0.7c1cc(nnc1)c2cc(cc(c2)Cl)NCCc3ccc(cc3)CCN4C[C@@H]([C@H]([C@@H]([C@H]4CO)O)O)O
ACDLabs 12.01Clc1cc(cc(c1)NCCc1ccc(CCN2CC(O)C(O)C(O)C2CO)cc1)c1cccnn1
CACTVS 3.385OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](O)CN1CCc2ccc(CCNc3cc(Cl)cc(c3)c4cccnn4)cc2
CACTVS 3.385OC[CH]1[CH](O)[CH](O)[CH](O)CN1CCc2ccc(CCNc3cc(Cl)cc(c3)c4cccnn4)cc2
FormulaC26 H31 Cl N4 O4
Name(2R,3R,4R,5S)-1-{2-[4-(2-{[(5M)-3-chloro-5-(pyridazin-3-yl)phenyl]amino}ethyl)phenyl]ethyl}-2-(hydroxymethyl)piperidine-3,4,5-triol
ChEMBL
DrugBank
ZINC
PDB chain8ecw Chain B Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8ecw Structure-Based Design of Potent Iminosugar Inhibitors of Endoplasmic Reticulum alpha-Glucosidase I with Anti-SARS-CoV-2 Activity.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		F416 F417 F421 W423 D424 G584 D586 Y725
Binding residue
(residue number reindexed from 1)		F384 F385 F389 W391 D392 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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8ecw, PDBe:8ecw, PDBj:8ecw
PDBsum8ecw
PubMed36762932
UniProtG0SFD1

[Back to BioLiP]