7AXM

Structure of SARS-CoV-2 Main Protease bound to Pelitinib

Summary for 7AXM

• Entry DOI: 10.2210/pdb7axm/pdb
• Descriptor: 3C-like proteinase, DIMETHYL SULFOXIDE, (2E)-N-{4-[(3-chloro-4-fluorophenyl)amino]-3-cyano-7-ethoxyquinolin-6-yl}-4-(dimethylamino)but-2-enamide, ... (5 entities in total)
• Functional Keywords: inhibitor, complex, screen, sars-cov-2, peptide binding protein
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV, SARS-CoV-2)
• Total number of polymer chains: 1
• Total formula weight: 34675.09

Authors

Guenther, S.,Reinke, P.Y.A.,Oberthuer, D.,Yefanov, O.,Gelisio, L.,Ginn, H.,Lieske, J.,Domaracky, M.,Brehm, W.,Rahmani Mashour, A.,White, T.A.,Knoska, J.,Pena Esperanza, G.,Koua, F.,Tolstikova, A.,Groessler, M.,Fischer, P.,Hennicke, V.,Fleckenstein, H.,Trost, F.,Galchenkova, M.,Gevorkov, Y.,Li, C.,Awel, S.,Paulraj, L.X.,Ullah, N.,Falke, S.,Alves Franca, B.,Schwinzer, M.,Brognaro, H.,Werner, N.,Perbandt, M.,Tidow, H.,Seychell, B.,Beck, T.,Meier, S.,Doyle, J.J.,Giseler, H.,Melo, D.,Lane, T.J.,Dunkel, I.,Peck, A.,Saouane, S.,Hakanpaeae, J.,Meyer, J.,Noei, H.,Gribbon, P.,Ellinger, B.,Kuzikov, M.,Wolf, M.,Zhang, L.,Ehrt, C.,Pletzer-Zelgert, J.,Wollenhaupt, J.,Feiler, C.,Weiss, M.,Schulz, E.C.,Mehrabi, P.,Norton-Baker, B.,Schmidt, C.,Lorenzen, K.,Schubert, R.,Han, H.,Chari, A.,Fernandez Garcia, Y.,Turk, D.,Hilgenfeld, R.,Rarey, M.,Zaliani, A.,Chapman, H.N.,Pearson, A.,Betzel, C.,Meents, A. (deposition date: 2020-11-09, release date: 2020-12-02, Last modification date: 2024-01-31)

Primary citation

Gunther, S.,Reinke, P.Y.A.,Fernandez-Garcia, Y.,Lieske, J.,Lane, T.J.,Ginn, H.M.,Koua, F.H.M.,Ehrt, C.,Ewert, W.,Oberthuer, D.,Yefanov, O.,Meier, S.,Lorenzen, K.,Krichel, B.,Kopicki, J.D.,Gelisio, L.,Brehm, W.,Dunkel, I.,Seychell, B.,Gieseler, H.,Norton-Baker, B.,Escudero-Perez, B.,Domaracky, M.,Saouane, S.,Tolstikova, A.,White, T.A.,Hanle, A.,Groessler, M.,Fleckenstein, H.,Trost, F.,Galchenkova, M.,Gevorkov, Y.,Li, C.,Awel, S.,Peck, A.,Barthelmess, M.,Schlunzen, F.,Lourdu Xavier, P.,Werner, N.,Andaleeb, H.,Ullah, N.,Falke, S.,Srinivasan, V.,Franca, B.A.,Schwinzer, M.,Brognaro, H.,Rogers, C.,Melo, D.,Zaitseva-Doyle, J.J.,Knoska, J.,Pena-Murillo, G.E.,Mashhour, A.R.,Hennicke, V.,Fischer, P.,Hakanpaa, J.,Meyer, J.,Gribbon, P.,Ellinger, B.,Kuzikov, M.,Wolf, M.,Beccari, A.R.,Bourenkov, G.,von Stetten, D.,Pompidor, G.,Bento, I.,Panneerselvam, S.,Karpics, I.,Schneider, T.R.,Garcia-Alai, M.M.,Niebling, S.,Gunther, C.,Schmidt, C.,Schubert, R.,Han, H.,Boger, J.,Monteiro, D.C.F.,Zhang, L.,Sun, X.,Pletzer-Zelgert, J.,Wollenhaupt, J.,Feiler, C.G.,Weiss, M.S.,Schulz, E.C.,Mehrabi, P.,Karnicar, K.,Usenik, A.,Loboda, J.,Tidow, H.,Chari, A.,Hilgenfeld, R.,Uetrecht, C.,Cox, R.,Zaliani, A.,Beck, T.,Rarey, M.,Gunther, S.,Turk, D.,Hinrichs, W.,Chapman, H.N.,Pearson, A.R.,Betzel, C.,Meents, A.
X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease.
Science, 372:642-646, 2021

PubMed Abstract: The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput x-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (M), which is essential for viral replication. In contrast to commonly applied x-ray fragment screening experiments with molecules of low complexity, our screen tested already-approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to M In subsequent cell-based viral reduction assays, one peptidomimetic and six nonpeptidic compounds showed antiviral activity at nontoxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.

PubMed: 33811162
DOI: 10.1126/science.abf7945

Experimental method

X-RAY DIFFRACTION (1.4 Å)