5REU

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102395


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

    Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK. martin.walsh@diamond.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinase A306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T4D
Query on T4D

Download Ideal Coordinates CCD File 
A
2-[(4-acetylpiperazin-1-yl)sulfonyl]benzonitrile
C13 H15 N3 O3 S
GOCXXCRVJCAULM-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.233α = 90
b = 52.757β = 102.93
c = 44.543γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • 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