7M00

Structure of SARS-CoV-2 3CL protease in complex with inhibitor 13c

Summary for 7M00

• Entry DOI: 10.2210/pdb7m00/pdb
• Descriptor: 3C-like proteinase, (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, (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, ... (4 entities in total)
• Functional Keywords: covid-19, protease, severe acute respiratory syndrome coronavirus 2, sars-cov-2 3cl protease inhhibitors, hydrolase-inhibitor complex, hydrolase/inhibitor
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)
• Total number of polymer chains: 2
• Total formula weight: 70352.08

Authors

Lovell, S.,Kashipathy, M.M.,Battaile, K.P.,Chamandi, S.D.,Rathnayake, A.D.,Kim, Y.,Perera, K.D.,Jesri, A.R.M.,Nguyen, H.N.,Baird, M.A.,Miller, M.J.,Groutas, W.C.,Chang, K.O. (deposition date: 2021-03-10, release date: 2021-03-24, Last modification date: 2024-10-23)

Primary citation

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.
Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies.
J.Med.Chem., 64:17846-17865, 2021

PubMed Abstract: The COVID-19 pandemic is having a major impact on public health worldwide, and there is an urgent need for the creation of an armamentarium of effective therapeutics, including vaccines, biologics, and small-molecule therapeutics, to combat SARS-CoV-2 and emerging variants. Inspection of the virus life cycle reveals multiple viral- and host-based choke points that can be exploited to combat the virus. SARS-CoV-2 3C-like protease (3CLpro), an enzyme essential for viral replication, is an attractive target for therapeutic intervention, and the design of inhibitors of the protease may lead to the emergence of effective SARS-CoV-2-specific antivirals. We describe herein the results of our studies related to the application of X-ray crystallography, the Thorpe-Ingold effect, deuteration, and stereochemistry in the design of highly potent and nontoxic inhibitors of SARS-CoV-2 3CLpro.

PubMed: 34865476
DOI: 10.1021/acs.jmedchem.1c01037

Experimental method

X-RAY DIFFRACTION (2 Å)