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Structure paper

TitleStructure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies.
Journal, issue, pagesJ. Med. Chem., Vol. 64, Page 17846-17865, Year 2021
Publish dateMar 10, 2021 (structure data deposition date)
AuthorsDampalla, C.S. / Rathnayake, A.D. / Perera, K.D. / Jesri, A.M. / Nguyen, H.N. / Miller, M.J. / Thurman, H.A. / Zheng, J. / Kashipathy, M.M. / Battaile, K.P. ...Dampalla, C.S. / Rathnayake, A.D. / Perera, K.D. / Jesri, A.M. / Nguyen, H.N. / Miller, M.J. / Thurman, H.A. / Zheng, J. / Kashipathy, M.M. / Battaile, K.P. / Lovell, S. / Perlman, S. / Kim, Y. / Groutas, W.C. / Chang, K.O.
External linksJ. Med. Chem. / PubMed:34865476
MethodsX-ray diffraction
Resolution1.55 - 2.2 Å
Structure data

PDB-7lzt:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 8b
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-7lzu:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 12b
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-7lzv:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 19b
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-7lzw:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 20b (deuterated analog of 19b)
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-7lzx:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 1c
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-7lzy:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 3c
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-7lzz:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 5c
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-7m00:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 13c
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-7m01:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 14c
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-7m02:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 17c
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7m03:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 18c
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-7m04:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 21c
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

Chemicals

ChemComp-SO4:
SULFATE ION

ChemComp-YMY:
(1R,2S)-1-hydroxy-2-((S)-4-methyl-2-(((((1s,4S)-4-propylcyclohexyl)methoxy)carbonyl)amino)pentanamido)-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid

ChemComp-YN1:
(1S,2S)-1-hydroxy-2-((S)-4-methyl-2-(((((1s,4S)-4-propylcyclohexyl)methoxy)carbonyl)amino)pentanamido)-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid

ChemComp-HOH:
WATER

ChemComp-YKM:
(1R,2S)-2-((S)-2-((((S)-1-(4,4-difluorocyclohexyl)ethoxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid

ChemComp-YKP:
(1S,2S)-2-((S)-2-((((S)-1-(4,4-difluorocyclohexyl)ethoxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid

ChemComp-PG4:
TETRAETHYLENE GLYCOL / precipitant*YM

ChemComp-YLM:
(1R,2S)-2-((S)-2-((((4-fluorobenzyl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid

ChemComp-YLS:
(1S,2S)-2-((S)-2-((((4-fluorobenzyl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid

ChemComp-YMG:
(1S,2S)-2-((S)-2-((((4,4-dimethylcyclohexyl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid

ChemComp-YMD:
(1R,2S)-2-((S)-2-((((4,4-dimethylcyclohexyl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid

ChemComp-YMJ:
(1R,2S)-1-hydroxy-2-((S)-4-methyl-2-(((((1s,4S)-4-propylcyclohexyl)oxy)carbonyl)amino)pentanamido)-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid

ChemComp-YMM:
(1S,2S)-1-hydroxy-2-((S)-4-methyl-2-(((((1s,4S)-4-propylcyclohexyl)oxy)carbonyl)amino)pentanamido)-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid

ChemComp-YMS:
(1R,2S)-1-hydroxy-2-((S)-4-methyl-2-(((((1r,4S)-4-phenylcyclohexyl)oxy)carbonyl)amino)pentanamido)-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid

ChemComp-YMV:
(1S,2S)-1-hydroxy-2-((S)-4-methyl-2-(((((1r,4S)-4-phenylcyclohexyl)oxy)carbonyl)amino)pentanamido)-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid

ChemComp-YKA:
(1R,2S)-2-((S)-2-((((2-(4,4-difluorocyclohexyl)propan-2-yl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl)propane-1-sulfonic acid

ChemComp-YKD:
(1S,2S)-2-((S)-2-((((2-(4,4-difluorocyclohexyl)propan-2-yl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl)propane-1-sulfonic acid

ChemComp-YKV:
(1S,2S)-2-((S)-2-((((S)-1-(4,4-difluorocyclohexyl)-2-phenylethoxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid

ChemComp-YKS:
(1R,2S)-2-((S)-2-((((S)-1-(4,4-difluorocyclohexyl)-2-phenylethoxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid

ChemComp-YL7:
(1S,2S)-2-((S)-2-((((2-fluorobenzyl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl)propane-1-sulfonic acid

ChemComp-YKY:
(1R,2S)-2-((S)-2-((((2-fluorobenzyl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl)propane-1-sulfonic acid

ChemComp-YLD:
(1R,2S)-2-((S)-2-((((3-fluorobenzyl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid

ChemComp-YLJ:
(1S,2S)-2-((S)-2-((((3-fluorobenzyl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid

ChemComp-YLV:
(1R,2S)-1-hydroxy-2-((S)-4-methyl-2-((((perfluorophenyl)methoxy)carbonyl)amino)pentanamido)-3-((R)-2-oxo-2,3-dihydro-1H-pyrrol-3-yl)propane-1-sulfonic acid

ChemComp-YM1:
(1S,2S)-1-hydroxy-2-((S)-4-methyl-2-((((perfluorophenyl)methoxy)carbonyl)amino)pentanamido)-3-((R)-2-oxo-2,3-dihydro-1H-pyrrol-3-yl)propane-1-sulfonic acid

Source
  • severe acute respiratory syndrome coronavirus 2
KeywordsHYDROLASE/INHIBITOR / COVID-19 / PROTEASE / severe acute respiratory syndrome coronavirus 2 / SARS-CoV-2 3CL protease Inhhibitors / HYDROLASE-INHIBITOR complex

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