ISDA

Entry Detail

PDB ID:

5REB

Keywords:

HYDROLASE/HYDROLASE INHIBITOR

Title:

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2856434899

Biological Source:

Source Organism:

Severe acute respiratory syndrome coronavirus 2

Host Organism:

Escherichia coli

PDB Version:

Deposition Date:

2020-03-15

Release Date:

2020-03-25

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.68 Å

R-Value Free:

0.22

R-Value Work:

0.17

R-Value Observed:

0.17

Space Group:

C 1 2 1

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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

T0Y

Primary Citation

Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.

Douangamath, A, Fearon, D, Gehrtz, P, Krojer, T, Lukacik, P, Owen, C.D, Resnick, E, Strain-Damerell, C, Aimon, A, Abranyi-Balogh, P, Brandao-Neto, J, Carbery, A, Davison, G, Dias, A, Downes, T.D, Dunnett, L, Fairhead, M, Firth, J.D, Jones, S.P, Keeley, A, Keseru, G.M, Klein, H.F, Martin, M.P, Noble, M.E.M, O'Brien, P, Powell, A, Reddi, R.N, Skyner, R, Snee, M, Waring, M.J, Wild, C, London, N, von Delft, F, Walsh, M.A.Show

Nat Commun 11 5047 5047 (2020)

PMID: 33028810 DOI: 10.1038/s41467-020-18709-w

Abstact

COVID-19, caused by SARS-CoV-2, lacks effective therapeutics. Additionally, no antiviral drugs or vaccines were developed against the closely related coronavirus, SARS-CoV-1 or MERS-CoV, despite previous zoonotic outbreaks. To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. Our crystallographic screen identified 71 hits that span the entire active site, as well as 3 hits at the dimer interface. These structures reveal routes to rapidly develop more potent inhibitors through merging of covalent and non-covalent fragment hits; one series of low-reactivity, tractable covalent fragments were progressed to discover improved binders. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease.

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