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Structure paper

TitleStructure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease.
Journal, issue, pagesJ. Med. Chem., Vol. 65, Page 7818-7832, Year 2022
Publish dateDec 9, 2021 (structure data deposition date)
AuthorsDampalla, C.S. / Rathnayake, A.D. / Galasiti Kankanamalage, A.C. / Kim, Y. / Perera, K.D. / Nguyen, H.N. / Miller, M.J. / Madden, T.K. / Picard, H.R. / Thurman, H.A. ...Dampalla, C.S. / Rathnayake, A.D. / Galasiti Kankanamalage, A.C. / Kim, Y. / Perera, K.D. / Nguyen, H.N. / Miller, M.J. / Madden, T.K. / Picard, H.R. / Thurman, H.A. / Kashipathy, M.M. / Liu, L. / Battaile, K.P. / Lovell, S. / Chang, K.O. / Groutas, W.C.
External linksJ. Med. Chem. / PubMed:35638577
MethodsX-ray diffraction
Resolution1.45 - 2.1 Å
Structure data

PDB-7t3y:
Structure of MERS 3CL protease in complex with inhibitor 8c
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-7t3z:
Structure of MERS 3CL protease in complex with inhibitor 9c
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-7t40:
Structure of MERS 3CL protease in complex with inhibitor 10c
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-7t41:
Structure of MERS 3CL protease in complex with inhibitor 14c
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-7t42:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 2c
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-7t43:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 3c
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-7t44:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 4c
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-7t45:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 7c
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-7t46:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 8c
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-7t48:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 9c
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-7t49:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 10c
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-7t4a:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 11c
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7t4b:
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 14c
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

Chemicals

ChemComp-F5L:
(1R,2S)-1-hydroxy-2-{[N-({[7-(2-methylpropanoyl)-7-azaspiro[3.5]nonan-2-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

ChemComp-F8C:
(1S,2S)-1-hydroxy-2-{[N-({[7-(2-methylpropanoyl)-7-azaspiro[3.5]nonan-2-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

ChemComp-HOH:
WATER

ChemComp-FHS:
(1S,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-2-{[N-({[7-(phenylacetyl)-7-azaspiro[3.5]nonan-2-yl]oxy}carbonyl)-L-leucyl]amino}propane-1-sulfonic acid

ChemComp-FEY:
(1R,2S)-2-{[N-({[(2r,4R)-7-acetyl-7-azaspiro[3.5]non-5-en-2-yl]oxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

ChemComp-FV5:
(1R,2S)-1-hydroxy-2-{[N-({[7-(methanesulfonyl)-7-azaspiro[3.5]nonan-2-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

ChemComp-FVE:
(1S,2S)-1-hydroxy-2-{[N-({[7-(methanesulfonyl)-7-azaspiro[3.5]nonan-2-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

ChemComp-PG4:
TETRAETHYLENE GLYCOL / precipitant*YM

ChemComp-FWI:
(1R,2S)-2-{[N-({[1-(tert-butoxycarbonyl)azetidin-3-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3R)-2-oxo-2,3-dihydro-1H-pyrrol-3-yl]propane-1-sulfonic acid

ChemComp-FZI:
(1S,2S)-2-{[N-({[1-(tert-butoxycarbonyl)azetidin-3-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3R)-2-oxo-2,3-dihydro-1H-pyrrol-3-yl]propane-1-sulfonic acid

ChemComp-FIK:
(1S,2S)-2-[(N-{[(2-acetyl-2-azaspiro[3.3]heptan-6-yl)oxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

ChemComp-FIW:
(1R,2S)-1-hydroxy-2-{[N-({[2-(2-methylpropanoyl)-2-azaspiro[3.3]heptan-6-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

ChemComp-FN2:
(1S,2S)-1-hydroxy-2-[(N-{[(2-methyl-2-azaspiro[3.3]heptan-6-yl)oxy]carbonyl}-L-leucyl)amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

ChemComp-FP8:
(1R,2S)-1-hydroxy-2-[(N-{[(2-methyl-2-azaspiro[3.3]heptan-6-yl)oxy]carbonyl}-L-leucyl)amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

ChemComp-ESS:
(1R,2S)-2-[(N-{[(2-azaspiro[3.3]heptan-6-yl)oxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

ChemComp-ET6:
(1S,2S)-1-hydroxy-2-{[N-({[2-(methanesulfonyl)-2-azaspiro[3.3]heptan-6-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

ChemComp-EW9:
(1S,2S)-2-{[N-({[7-(tert-butoxycarbonyl)-7-azaspiro[3.5]nonan-2-yl]oxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

ChemComp-CL:
Unknown entry

ChemComp-EQS:
(1S,2S)-2-[(N-{[(7-cyano-7-azaspiro[3.5]nonan-2-yl)oxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

ChemComp-EO6:
(1R,2S)-2-[(N-{[(7-cyano-7-azaspiro[3.5]nonan-2-yl)oxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

ChemComp-PO4:
PHOSPHATE ION

Source
  • middle east respiratory syndrome-related coronavirus (isolate united kingdom/h123990006/2012)
  • severe acute respiratory syndrome coronavirus 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEASE / MERS 3CL protease Inhhibitors / hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex / COVID-19 / severe acute respiratory syndrome coronavirus 2 / SARS-CoV-2 3CL protease Inhhibitors

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