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Structure paper

TitleStructure-Based Design of Potent Iminosugar Inhibitors of Endoplasmic Reticulum alpha-Glucosidase I with Anti-SARS-CoV-2 Activity.
Journal, issue, pagesJ. Med. Chem., Vol. 66, Page 2744-2760, Year 2023
Publish dateJun 22, 2021 (structure data deposition date)
AuthorsKarade, S.S. / Franco, E.J. / Rojas, A.C. / Hanrahan, K.C. / Kolesnikov, A. / Yu, W. / MacKerell Jr., A.D. / Hill, D.C. / Weber, D.J. / Brown, A.N. ...Karade, S.S. / Franco, E.J. / Rojas, A.C. / Hanrahan, K.C. / Kolesnikov, A. / Yu, W. / MacKerell Jr., A.D. / Hill, D.C. / Weber, D.J. / Brown, A.N. / Treston, A.M. / Mariuzza, R.A.
External linksJ. Med. Chem. / PubMed:36762932
MethodsX-ray diffraction
Resolution1.905 - 2.8 Å
Structure data

PDB-7r6j:
Co-crystal structure of Chaetomium glucosidase with compound 1
Method: X-RAY DIFFRACTION / Resolution: 1.905 Å

PDB-7rd2:
Co-crystal structure of Chaetomium glucosidase with compound 2
Method: X-RAY DIFFRACTION / Resolution: 2.61 Å

PDB-7rev:
Co-crystal structure of Chaetomium glucosidase with compound 3
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-8e3j:
Co-crystal structure of Chaetomium glucosidase with compound 4
Method: X-RAY DIFFRACTION / Resolution: 2.71 Å

PDB-8e3p:
Co-crystal structure of Chaetomium glucosidase with compound 5
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-8e4i:
Co-crystal structure of Chaetomium glucosidase with compound 6
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-8e4k:
Co-crystal structure of Chaetomium glucosidase with compound 7
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-8e4z:
Co-crystal structure of Chaetomium glucosidase with compound 8
Method: X-RAY DIFFRACTION / Resolution: 2.37 Å

PDB-8e5u:
Co-crystal structure of Chaetomium glucosidase with compound 9
Method: X-RAY DIFFRACTION / Resolution: 2.33 Å

PDB-8e6g:
Co-crystal structure of Chaetomium glucosidase with compound 10
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-8ecw:
Co-crystal structure of Chaetomium glucosidase with compound 11
Method: X-RAY DIFFRACTION / Resolution: 2.25 Å

PDB-8egv:
Co-crystal structure of Chaetomium glucosidase with compound 12
Method: X-RAY DIFFRACTION / Resolution: 2.09 Å

PDB-8ehp:
Co-crystal structure of Chaetomium glucosidase with compound 13
Method: X-RAY DIFFRACTION / Resolution: 2.68 Å

PDB-8eid:
Co-crystal structure of Chaetomium glucosidase with compound 14
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-8ekn:
Co-crystal structure of Chaetomium glucosidase with compound 15
Method: X-RAY DIFFRACTION / Resolution: 2.29 Å

PDB-8ele:
Co-crystal structure of Chaetomium glucosidase with compound 16
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-8epj:
Co-crystal structure of Chaetomium glucosidase with compound 17
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-8epo:
Co-crystal structure of Chaetomium glucosidase with compound 18
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-8epr:
Co-crystal structure of Chaetomium glucosidase with compound 19
Method: X-RAY DIFFRACTION / Resolution: 1.99 Å

PDB-8eq7:
Co-crystal structure of Chaetomium glucosidase with compound 20
Method: X-RAY DIFFRACTION / Resolution: 2.21 Å

PDB-8eqx:
Co-crystal structure of Chaetomium glucosidase with compound 21
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-8er4:
Co-crystal structure of Chaetomium glucosidase with compound 23
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-8etl:
Co-crystal structure of Chaetomium glucosidase with compound 24
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-8eto:
Co-crystal structure of Chaetomium glucosidase with compound 25
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-8eud:
Co-crystal structure of Chaetomium glucosidase with compound 22
Method: X-RAY DIFFRACTION / Resolution: 2.37 Å

PDB-8eur:
Co-crystal structure of Chaetomium glucosidase with compound 26
Method: X-RAY DIFFRACTION / Resolution: 2.61 Å

PDB-8eut:
Co-crystal structure of Chaetomium glucosidase with compound 27
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-8eux:
Co-crystal structure of Chaetomium glucosidase with compound 28
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

Chemicals

ChemComp-2I7:
(2R,3R,4R,5S)-2-(hydroxymethyl)-1-[(3-{[3-methyl-5-(pyrimidin-2-yl)anilino]methyl}phenyl)methyl]piperidine-3,4,5-triol

ChemComp-GOL:
GLYCEROL

ChemComp-SO4:
SULFATE ION

ChemComp-BTB:
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM

ChemComp-HOH:
WATER

ChemComp-5X7:
(2R,3R,4R,5S)-1-{[4-({4-[(2R,6S)-2,6-dimethylmorpholin-4-yl]-2-nitroanilino}methyl)phenyl]methyl}-2-(hydroxymethyl)piperidine-3,4,5-triol

ChemComp-5RK:
(2R,3R,4R,5S)-1-[(4-{[4-(furan-2-yl)-2-methylanilino]methyl}phenyl)methyl]-2-(hydroxymethyl)piperidine-3,4,5-triol

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-UGO:
(2R,3R,4R,5S)-2-(hydroxymethyl)-1-{6-[2-nitro-4-(pyrimidin-2-yl)anilino]hexyl}piperidine-3,4,5-triol

ChemComp-UF6:
(2S,3S,4S,5R)-2-(hydroxymethyl)-1-{6-[3-nitro-5-(pyridin-4-yl)anilino]hexyl}piperidine-3,4,5-triol

ChemComp-UIJ:
(2R,3R,4R,5S)-2-(hydroxymethyl)-1-(6-{[(4P)-4-(5-methyl-1,2,4-oxadiazol-3-yl)-2-nitrophenyl]amino}hexyl)piperidine-3,4,5-triol

ChemComp-UIO:
(2R,3R,4R,5S)-2-(hydroxymethyl)-1-[6-({(4M)-4-[2-(morpholin-4-yl)pyrimidin-4-yl]-2-nitrophenyl}amino)hexyl]piperidine-3,4,5-triol

ChemComp-UKF:
(2R,3R,4R,5S)-1-(6-{[(4P)-4-(5-cyclobutyl-1,2,4-oxadiazol-3-yl)-2-nitrophenyl]amino}hexyl)-2-(hydroxymethyl)piperidine-3,4,5-triol

ChemComp-UPH:
(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

ChemComp-UQH:
(2R,3R,4R,5S)-1-(6-{[(5M)-3-cyclopropyl-5-(pyridazin-3-yl)phenyl]amino}hexyl)-2-(hydroxymethyl)piperidine-3,4,5-triol

ChemComp-X5B:
(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

ChemComp-WJF:
(2R,3R,4R,5S)-1-{2-[4-(2-{[(5M)-3-chloro-5-(1,2,4-oxadiazol-3-yl)phenyl]amino}ethyl)phenyl]ethyl}-2-(hydroxymethyl)piperidine-3,4,5-triol

ChemComp-WJO:
(2R,3R,4R,5S)-2-(hydroxymethyl)-1-[(4-{[4-(morpholin-4-yl)anilino]methyl}phenyl)methyl]piperidine-3,4,5-triol

ChemComp-WJT:
(2R,3R,4R,5S)-2-(hydroxymethyl)-1-{[4-({[(5P)-3-(methanesulfonyl)-5-(pyridazin-3-yl)phenyl]amino}methyl)phenyl]methyl}piperidine-3,4,5-triol

ChemComp-WLQ:
(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

ChemComp-WM0:
(2R,3R,4R,5S)-2-(hydroxymethyl)-1-{[4-({2-nitro-4-[(1R,5S)-3-oxa-8-azabicyclo[3.2.1]octan-8-yl]anilino}methyl)phenyl]methyl}piperidine-3,4,5-triol

ChemComp-WQU:
(2R,3R,4R,5S)-2-(hydroxymethyl)-1-[(3-{[4-(morpholin-4-yl)-2-nitroanilino]methyl}phenyl)methyl]piperidine-3,4,5-triol

ChemComp-WQZ:
(3P)-3-(5,6-dihydro-1,4-dioxin-2-yl)-5-{[(3-{[(2R,3R,4R,5S)-3,4,5-trihydroxy-2-(hydroxymethyl)piperidin-1-yl]methyl}phenyl)methyl]amino}benzonitrile

ChemComp-WSW:
(2R,3R,4R,5S)-2-(hydroxymethyl)-1-{[3-({[(5M)-3-(methanesulfonyl)-5-(pyridazin-3-yl)phenyl]amino}methyl)phenyl]methyl}piperidine-3,4,5-triol

ChemComp-WT0:
(2R,3R,4R,5S)-1-[(3-{[3-bromo-5-(methanesulfonyl)anilino]methyl}phenyl)methyl]-2-(hydroxymethyl)piperidine-3,4,5-triol

ChemComp-WT5:
(2R,3R,4R,5S)-2-(hydroxymethyl)-1-{[6-({[(5M)-3-methyl-5-(1H-pyrrol-2-yl)phenyl]amino}methyl)pyridin-2-yl]methyl}piperidine-3,4,5-triol

ChemComp-XG5:
(2R,3R,4R,5S)-1-(2-{6-[2-(4-azido-2-nitroanilino)ethyl]pyrazin-2-yl}ethyl)-2-(hydroxymethyl)piperidine-3,4,5-triol

ChemComp-VND:
(1S,2S,3R,4S,5S)-5-(butylamino)-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol

ChemComp-W9V:
(1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-{[(5Z)-6-{[2-nitro-4-(2H-1,2,3-triazol-2-yl)phenyl]amino}hex-5-en-1-yl]amino}cyclohexane-1,2,3,4-tetrol

ChemComp-WUR:
(2R,3R,4R,5S)-2-(hydroxymethyl)-1-{6-[2-methyl-5-(pyrimidin-2-yl)-1H-benzimidazol-1-yl]hexyl}piperidine-3,4,5-triol

ChemComp-WAS:
2-{[2-nitro-4-(triazan-1-yl)phenyl]amino}ethyl (2-{[(1S,2S,3R,4S,5S)-2,3,4,5-tetrahydroxy-5-(hydroxymethyl)cyclohexyl]amino}ethyl)carbamate

ChemComp-WV5:
(2R,3R,4R,5S)-1-[8-(furan-2-yl)octyl]-2-(hydroxymethyl)piperidine-3,4,5-triol

ChemComp-WV9:
(2R,3R,4R,5S)-2-(hydroxymethyl)-1-{5-[4-(2-methoxyethyl)phenyl]pentyl}piperidine-3,4,5-triol

Source
  • chaetomium thermophilum (strain dsm 1495 / cbs 144.50 / imi 039719) (fungus)
  • thermochaetoides thermophila (fungus)
  • thermochaetoides thermophila dsm 1495 (fungus)
KeywordsHYDROLASE/INHIBITOR / alpha glucosidase I / Hydrolase / Inhibitor complex / HYDROLASE-INHIBITOR complex / HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex

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