5S49

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z56866006


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.03 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.

Schuller, M.Correy, G.J.Gahbauer, S.Fearon, D.Wu, T.Diaz, R.E.Young, I.D.Carvalho Martins, L.Smith, D.H.Schulze-Gahmen, U.Owens, T.W.Deshpande, I.Merz, G.E.Thwin, A.C.Biel, J.T.Peters, J.K.Moritz, M.Herrera, N.Kratochvil, H.T.Aimon, A.Bennett, J.M.Brandao Neto, J.Cohen, A.E.Dias, A.Douangamath, A.Dunnett, L.Fedorov, O.Ferla, M.P.Fuchs, M.R.Gorrie-Stone, T.J.Holton, J.M.Johnson, M.G.Krojer, T.Meigs, G.Powell, A.J.Rack, J.G.M.Rangel, V.L.Russi, S.Skyner, R.E.Smith, C.A.Soares, A.S.Wierman, J.L.Zhu, K.O'Brien, P.Jura, N.Ashworth, A.Irwin, J.J.Thompson, M.C.Gestwicki, J.E.von Delft, F.Shoichet, B.K.Fraser, J.S.Ahel, I.

(2021) Sci Adv 7

  • DOI: 10.1126/sciadv.abf8711
  • Primary Citation of Related Structures:  
    5RS7, 5RS8, 5RS9, 5RSB, 5RSC, 5RSD, 5RSE, 5RSF, 5RSG, 5RSH, 5RSI, 5RSJ, 5RSK, 5RSL, 5RSM, 5RSN, 5RSO, 5RSP, 5RSQ, 5RSR, 5RSS, 5RST, 5RSU, 5RSV, 5RSW, 5RSX, 5RSY, 5RSZ, 5RT0, 5RT1, 5RT2, 5RT3, 5RT4, 5RT5, 5RT6, 5RT7, 5RT8, 5RT9, 5RTA, 5RTB, 5RTC, 5RTD, 5RTE, 5RTF, 5RTG, 5RTH, 5RTI, 5RTJ, 5RTK, 5RTL

  • PubMed Abstract: 
  • The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) macrodomain within the nonstructural protein 3 counteracts host-mediated antiviral adenosine diphosphate-ribosylation signaling. This enzyme is a promising antiviral target because catalytic mutations render viruses nonpathogenic ...

    The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) macrodomain within the nonstructural protein 3 counteracts host-mediated antiviral adenosine diphosphate-ribosylation signaling. This enzyme is a promising antiviral target because catalytic mutations render viruses nonpathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of 2533 diverse fragments resulted in 214 unique macrodomain-binders. An additional 60 molecules were selected from docking more than 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several fragment hits were confirmed by solution binding using three biophysical techniques (differential scanning fluorimetry, homogeneous time-resolved fluorescence, and isothermal titration calorimetry). The 234 fragment structures explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.


    Organizational Affiliation

    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK. ivan.ahel@path.ox.ac.uk jfraser@fraserlab.com bshoichet@gmail.com frank.von-delft@diamond.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 3A, B169Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22.69 (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)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3TR (Subject of Investigation/LOI)
Query on 3TR

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
F [auth B]
3-AMINO-1,2,4-TRIAZOLE
C2 H4 N4
KLSJWNVTNUYHDU-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.03 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.948α = 90
b = 87.948β = 90
c = 38.598γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
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: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Structure summary
  • Version 1.2: 2021-07-07
    Changes: Database references