7AVD | pdb_00007avd

Structure of SARS-CoV-2 Main Protease bound to SEN1269 ligand

• PDB DOI: https://doi.org/10.2210/pdb7AVD/pdb

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-11-05 Released: 2020-12-02 
• Deposition Author(s): Koua, F., Guenther, S., Reinke, P., Oberthuer, D., Yefanov, O., Gelisio, L., Ginn, H., Lieske, J., Ewert, W., Domaracky, M., Brehm, W., Rahmani Mashour, A., White, T.A., Knoska, J., Pena Esperanza, G., 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., Dunkel, I., Lane, T.J., 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.
• Funding Organization(s): German Research Foundation (DFG), European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease.

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.

(2021) Science 372: 642-646

• PubMed: 33811162 
• DOI: https://doi.org/10.1126/science.abf7945
• Primary Citation Related Structures: 
  6YNQ, 6YVF, 7A1U, 7ABU, 7ADW, 7AF0, 7AGA, 7AHA, 7AK4, 7AKU, 7AMJ, 7ANS, 7AOL, 7AP6, 7APH, 7AQE, 7AQI, 7AQJ, 7AR5, 7AR6, 7ARF, 7AVD, 7AWR, 7AWS, 7AWU, 7AWW, 7AX6, 7AXM, 7AXO, 7AY7, 7B83, 7NEV


• 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 ^pro ), 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 ^pro 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.

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Organizational Affiliation: 
• Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany. [e-mail] [e-mail].
Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany.
Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
Universität Hamburg, Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany.
Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany.
European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany.
Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, 20251 Hamburg, Germany.
Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany.
Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany.
Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany.
Department of Chemistry, UC Irvine, Irvine, CA 92697-2025, USA.
Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
Vision Systems, Hamburg University of Technology, 21071 Hamburg, Germany.
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany.
Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany.
Dompé Farmaceutici SpA, 67100 L'Aquila, Italy.
EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany.
Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany.
Hauptmann Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.
German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany.
Helmholtz Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany.
Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia.
Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia.
Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany.
Research Group for Structural Biochemistry and Mechanisms, Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Schneiderberg 38, 30167 Hannover, Germany.
Universität Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany.
Universität Hamburg, Department of Physics, Luruper Chaussee 149, 22761 Hamburg, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 68.04 kDa 
• Atom Count: 5,412 
• Modeled Residue Count: 612 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S1W (Subject of Investigation/LOI)	D [auth B]	3-[[5-[3-(dimethylamino)phenoxy]pyrimidin-2-yl]amino]phenol C18 H18 N4 O2 MFPAAKZZUIRMKR-UHFFFAOYSA-N
CL	C [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.552	α = 90
b = 53.857	β = 100.61
c = 114.731	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-02 
Deposition Author(s): Koua, F., Guenther, S., Reinke, P., Oberthuer, D., Yefanov, O., Gelisio, L., Ginn, H., Lieske, J., Ewert, W., Domaracky, M., Brehm, W., Rahmani Mashour, A., White, T.A., Knoska, J., Pena Esperanza, G., 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., Dunkel, I., Lane, T.J., 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.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	EXC 2056-project ID: 39071
European Commission	Germany	EU Project 101003551-EXS

Revision History  

• Version 1.0: 2020-12-02
  Type: Initial release
  
• Version 1.1: 2020-12-09
  Changes: Database references
• Version 1.2: 2021-04-14
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.3: 2021-05-19
  Changes: Database references
• Version 1.4: 2024-01-31
  Changes: Data collection, Database references, Refinement description