Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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: 34.27 kDa 
• Atom Count: 2731 
• Residue Count: 304 
• Unique protein chains: 1

5RE8

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2737076969

• DOI: 10.2210/pdb5RE8/pdb
• Deposition Group: G_1002151 (changed state)

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


• Deposited: 2020-03-15 Released: 2020-03-25 
• Deposition Author(s): Fearon, D., Owen, C.D., Douangamath, A., Lukacik, P., Powell, A.J., Strain-Damerell, C.M., Resnick, E., Krojer, T., Gehrtz, P., Wild, C., Aimon, A., Brandao-Neto, J., Carbery, A., Dunnett, L., Skyner, R., Snee, M., London, N., Walsh, M.A., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.248 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 

Literature

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.

(2020) Nat Commun 11: 5047-5047

• PubMed: 33028810 
• DOI: 10.1038/s41467-020-18709-w
• Primary Citation of Related Structures:  
  5R84, 5R83, 5R7Y, 5R80, 5R82, 5R81, 5R7Z, 5REA, 5REC, 5REB


• PubMed Abstract: 
  

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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Organizational Affiliation: 

Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK. [e-mail].

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), 3.1 (UniProt), 2.1.1 (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
T0V	A	1-(3-fluorophenyl)-N-[(furan-2-yl)methyl]methanamine C12 H12 F N O AFHNQIFVWMDQAM-UHFFFAOYSA-N
DMS	A	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.248 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.962	α = 90
b = 52.752	β = 102.99
c = 44.174	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2020-03-15 
• Released Date: 2020-03-25 
Deposition Author(s): Fearon, D., Owen, C.D., Douangamath, A., Lukacik, P., Powell, A.J., Strain-Damerell, C.M., Resnick, E., Krojer, T., Gehrtz, P., Wild, C., Aimon, A., Brandao-Neto, J., Carbery, A., Dunnett, L., Skyner, R., Snee, M., London, N., Walsh, M.A., von Delft, F.

Revision History 

• Version 1.0: 2020-03-25
  Type: Initial release
  
• Version 1.1: 2020-04-08
  Changes: Database references, Structure summary
• Version 1.2: 2020-05-06
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.3: 2021-01-27
  Changes: Structure summary
• Version 1.4: 2021-02-24
  Changes: Database references