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Structure paper

TitleDevelopment of a GC-376 Based Peptidomimetic PROTAC as a Degrader of 3-Chymotrypsin-like Protease of SARS-CoV-2.
Journal, issue, pagesAcs Med. Chem. Lett., Vol. 15, Page 250-257, Year 2024
Publish dateMar 28, 2023 (structure data deposition date)
AuthorsGrifagni, D. / Lenci, E. / De Santis, A. / Orsetti, A. / Barracchia, C.G. / Tedesco, F. / Bellini Puglielli, R. / Lucarelli, F. / Lauriola, A. / Assfalg, M. ...Grifagni, D. / Lenci, E. / De Santis, A. / Orsetti, A. / Barracchia, C.G. / Tedesco, F. / Bellini Puglielli, R. / Lucarelli, F. / Lauriola, A. / Assfalg, M. / Cantini, F. / Calderone, V. / Guardavaccaro, D. / Trabocchi, A. / D'Onofrio, M. / Ciofi-Baffoni, S.
External linksAcs Med. Chem. Lett. / PubMed:38352832
MethodsX-ray diffraction
Resolution2 - 2.31 Å
Structure data

PDB-8okb:
SARS-CoV2 NSP5 in complex with a peptidomimetic ligand
Method: X-RAY DIFFRACTION / Resolution: 2.31 Å

PDB-8okc:
SARS-CoV2 NSP5 in complex with a GC-376 based peptidomimetic PROTAC
Method: X-RAY DIFFRACTION / Resolution: 2 Å

Chemicals

ChemComp-VQR:
methyl (4~{S})-4-[[(2~{S})-4-methyl-2-(phenylmethoxycarbonylamino)pentanoyl]amino]-5-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]pentanoate

ChemComp-HOH:
WATER

ChemComp-VQN:
(phenylmethyl) ~{N}-[(2~{R})-1-[[(~{Z},2~{S})-5-[4-[[1-[2-[(3~{R})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1,3-bis(oxidanylidene)isoindol-5-yl]piperidin-4-yl]methyl]piperazin-1-yl]-5-oxidanylidene-1-[(3~{R})-2-oxidanylidenepyrrolidin-3-yl]pent-3-en-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate

Source
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN / NSP5 / SARS-CoV2 / 3CLpro / PROTAC

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