5RVG

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000400552187_N3

• PDB DOI:  https://doi.org/10.2210/pdb5RVG/pdb
• Deposition Group: G_1002171 (changed state) ExploreG_1002171

• Classification: VIRAL PROTEIN, HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-09-28 Released: 2020-12-16 
• Deposition Author(s): Correy, G.J., Young, I.D., Thompson, M.C., Fraser, J.S.
• Funding Organization(s): National Science Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.179 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

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

• PubMed: 33853786 
• DOI: https://doi.org/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. 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. [e-mail] [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.85 kDa 
• Atom Count: 3,083 
• Modelled Residue Count: 336 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A, B	169	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-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), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
W8J (Subject of Investigation/LOI)	C [auth A], D [auth A]	3-{3-[(3S)-oxolan-3-yl]propyl}-3H-purin-6-amine C12 H17 N5 O GTHFXQJDSWIMIA-VIFPVBQESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.179 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: P 4₃
• Diffraction Data: https://doi.org/10.18430/m35rvg

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.784	α = 90
b = 88.784	β = 90
c = 39.481	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Correy, G.J., Young, I.D., Thompson, M.C., Fraser, J.S.

---

Funding Organization	Location	Grant Number
National Science Foundation	United States	2031205

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2021-01-27
  Changes: Structure summary
• Version 1.2: 2021-05-12
  Changes: Structure summary
• Version 1.3: 2021-06-09
  Changes: Structure summary
• Version 1.4: 2022-05-25
  Changes: Database references