ISDA

Entry Detail

PDB ID:

7GAY

Keywords:

Title:

Group deposition SARS-CoV-2 main protease in complex with inhibitors from the COVID Moonshot -- Crystal Structure of SARS-CoV-2 main protease in complex with BEN-DND-031a96cc-8 (Mpro-x10022)

Biological Source:

Source Organism:

Severe acute respiratory syndrome coronavirus 2

Host Organism:

Escherichia coli

PDB Version:

Deposition Date:

2023-08-11

Release Date:

2023-11-08

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.30 Å

R-Value Free:

0.19

R-Value Work:

0.15

R-Value Observed:

0.15

Space Group:

C 1 2 1

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:3C-like proteinase
Chain IDs:A
Chain Length:306
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTD1 Pfam ID:PF05409 EC:2.7.7.48

Ligand Molecules

DMS

KJO

Primary Citation

Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors.

Boby, M.L, Fearon, D, Ferla, M, Filep, M, Koekemoer, L, Robinson, M.C, Chodera, J.D, Lee, A.A, London, N, von Delft, A, von Delft, F, Achdout, H, Aimon, A, Alonzi, D.S, Arbon, R, Aschenbrenner, J.C, Balcomb, B.H, Bar-David, E, Barr, H, Ben-Shmuel, A, Bennett, J, Bilenko, V.A, Borden, B, Boulet, P, Bowman, G.R, Brewitz, L, Brun, J, Bvnbs, S, Calmiano, M, Carbery, A, Carney, D.W, Cattermole, E, Chang, E, Chernyshenko, E, Clyde, A, Coffland, J.E, Cohen, G, Cole, J.C, Contini, A, Cox, L, Croll, T.I, Cvitkovic, M, De Jonghe, S, Dias, A, Donckers, K, Dotson, D.L, Douangamath, A, Duberstein, S, Dudgeon, T, Dunnett, L.E, Eastman, P, Erez, N, Eyermann, C.J, Fairhead, M, Fate, G, Fedorov, O, Fernandes, R.S, Ferrins, L, Foster, R, Foster, H, Fraisse, L, Gabizon, R, Garcia-Sastre, A, Gawriljuk, V.O, Gehrtz, P, Gileadi, C, Giroud, C, Glass, W.G, Glen, R.C, Glinert, I, Godoy, A.S, Gorichko, M, Gorrie-Stone, T, Griffen, E.J, Haneef, A, Hassell Hart, S, Heer, J, Henry, M, Hill, M, Horrell, S, Huang, Q.Y.J, Huliak, V.D, Hurley, M.F.D, Israely, T, Jajack, A, Jansen, J, Jnoff, E, Jochmans, D, John, T, Kaminow, B, Kang, L, Kantsadi, A.L, Kenny, P.W, Kiappes, J.L, Kinakh, S.O, Kovar, B, Krojer, T, La, V.N.T, Laghnimi-Hahn, S, Lefker, B.A, Levy, H, Lithgo, R.M, Logvinenko, I.G, Lukacik, P, Macdonald, H.B, MacLean, E.M, Makower, L.L, Malla, T.R, Marples, P.G, Matviiuk, T, McCorkindale, W, McGovern, B.L, Melamed, S, Melnykov, K.P, Michurin, O, Miesen, P, Mikolajek, H, Milne, B.F, Minh, D, Morris, A, Morris, G.M, Morwitzer, M.J, Moustakas, D, Mowbray, C.E, Nakamura, A.M, Neto, J.B, Neyts, J, Nguyen, L, Noske, G.D, Oleinikovas, V, Oliva, G, Overheul, G.J, Owen, C.D, Pai, R, Pan, J, Paran, N, Payne, A.M, Perry, B, Pingle, M, Pinjari, J, Politi, B, Powell, A, Psenak, V, Pulido, I, Puni, R, Rangel, V.L, Reddi, R.N, Rees, P, Reid, S.P, Reid, L, Resnick, E, Ripka, E.G, Robinson, R.P, Rodriguez-Guerra, J, Rosales, R, Rufa, D.A, Saar, K, Saikatendu, K.S, Salah, E, Schaller, D, Scheen, J, Schiffer, C.A, Schofield, C.J, Shafeev, M, Shaikh, A, Shaqra, A.M, Shi, J, Shurrush, K, Singh, S, Sittner, A, Sjo, P, Skyner, R, Smalley, A, Smeets, B, Smilova, M.D, Solmesky, L.J, Spencer, J, Strain-Damerell, C, Swamy, V, Tamir, H, Taylor, J.C, Tennant, R.E, Thompson, W, Thompson, A, Tomasio, S, Tomlinson, C.W.E, Tsurupa, I.S, Tumber, A, Vakonakis, I, van Rij, R.P, Vangeel, L, Varghese, F.S, Vaschetto, M, Vitner, E.B, Voelz, V, Volkamer, A, Walsh, M.A, Ward, W, Weatherall, C, Weiss, S, White, K.M, Wild, C.F, Witt, K.D, Wittmann, M, Wright, N, Yahalom-Ronen, Y, Yilmaz, N.K, Zaidmann, D, Zhang, I, Zidane, H, Zitzmann, N, Zvornicanin, S.N.Show

Science 382 eabo7201 eabo7201 (2023)

PMID: 37943932 DOI: 10.1126/science.abo7201

Abstact

We report the results of the COVID Moonshot, a fully open-science, crowdsourced, and structure-enabled drug discovery campaign targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease. We discovered a noncovalent, nonpeptidic inhibitor scaffold with lead-like properties that is differentiated from current main protease inhibitors. Our approach leveraged crowdsourcing, machine learning, exascale molecular simulations, and high-throughput structural biology and chemistry. We generated a detailed map of the structural plasticity of the SARS-CoV-2 main protease, extensive structure-activity relationships for multiple chemotypes, and a wealth of biochemical activity data. All compound designs (>18,000 designs), crystallographic data (>490 ligand-bound x-ray structures), assay data (>10,000 measurements), and synthesized molecules (>2400 compounds) for this campaign were shared rapidly and openly, creating a rich, open, and intellectual property-free knowledge base for future anticoronavirus drug discovery.

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Primary Citation of related structures