6YVF

Structure of SARS-CoV-2 Main Protease bound to AZD6482.

• PDB DOI:  https://doi.org/10.2210/pdb6YVF/pdb

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


• Deposited: 2020-04-28 Released: 2020-05-20 
• Deposition Author(s): Guenther, S., Reinke, P., 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., 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: 1.60 Å
• R-Value Free: 0.208 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 

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 of 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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Related Citations: 

• Inhibition of SARS-CoV-2 main protease by allosteric drug-binding
  Guenther, 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.,, Schluenzen , F.,, Paulraj , L.X.,, Werner , N.,, Andaleeb , H.,, Ullah , N.,, Falke , S.,, Srinivasan, V.,, Franca , B.,, Schwinzer , M.,, Brognaro , H.,, Rogers , C.,, Melo , D.,, Doyle , J.J.,, Knoska , J.,, Pena Murillo, G.E.,, Rahmani Mashhour, A.,, Guicking , F.,, Hennicke , V.,, Fischer , P.,, Hakanpaeae , J.,, Meyer , J.,, Gribbon , P.,, Ellinger , B.,, Kuzikov , M.,, Wolf , M.,, Burenkov, G.,, von Stetten, D.,, Pompidor, G.,, Bento, I.,, Panneerselvam, S.,, Karpics, I.,, Schneider , T.R.,, Garcia Alai, M.,, Niebling, S.,, Guenther , C.,, Schmidt , C.,, Schubert , R.,, Han , H.,, Boger, J.,, Monteiro , D.,, Zhang, L.,, Sun, X.,, Pletzer-Zelgert , J.,, Wollenhaupt , J.,, Feiler , C.,, Weiss , M.,, 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.,, Guenther , S.,, Turk , D.,, Hinrichs , W.,, Chapman , H.N.,, Pearson , A.,, Betzel , C.,, Meents , A.
  (2020) Biorxiv --: --

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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].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.98 kDa 
• Atom Count: 2,890 
• Modelled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A82 (Subject of Investigation/LOI)	B [auth A]	2-[[(1R)-1-(7-methyl-2-morpholin-4-yl-4-oxidanylidene-pyrido[1,2-a]pyrimidin-9-yl)ethyl]amino]benzoic acid C22 H24 N4 O4 IRTDIKMSKMREGO-OAHLLOKOSA-N
PEG	I [auth A], J [auth A], K [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS	E [auth A], F [auth A], G [auth A], H [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CA	L [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.208 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.153	α = 90
b = 53.645	β = 102.313
c = 44.595	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-20 
Deposition Author(s): Guenther, S., Reinke, P., 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., 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 390715994
European Commission	European Union	EU project 101003551 - EXSCALATE4CoV (E4C)

Revision History  

• Version 1.0: 2020-05-20
  Type: Initial release
  
• Version 1.1: 2020-12-02
  Changes: Database references
• Version 1.2: 2020-12-09
  Changes: Database references
• Version 1.3: 2021-04-14
  Changes: Author supporting evidence, Database references, Source and taxonomy, Structure summary
• Version 1.4: 2021-05-19
  Changes: Database references