8RF3

Crystal structure of N-terminal SARS-CoV-2 nsp1 in complex with fragment hit 7G3 refined against the anomalous diffraction data


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

Starting Model: experimental
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Literature

High-confidence placement of low-occupancy fragments into electron density using the anomalous signal of sulfur and halogen atoms.

Ma, S.Damfo, S.Bowler, M.W.Mykhaylyk, V.Kozielski, F.

(2024) Acta Crystallogr D Struct Biol 80: 451-463

  • DOI: https://doi.org/10.1107/S2059798324004480
  • Primary Citation of Related Structures:  
    8RF2, 8RF3, 8RF4, 8RF5, 8RF6, 8RF8, 8RFC, 8RFD, 8RFF

  • PubMed Abstract: 

    Fragment-based drug design using X-ray crystallography is a powerful technique to enable the development of new lead compounds, or probe molecules, against biological targets. This study addresses the need to determine fragment binding orientations for low-occupancy fragments with incomplete electron density, an essential step before further development of the molecule. Halogen atoms play multiple roles in drug discovery due to their unique combination of electronegativity, steric effects and hydrophobic properties. Fragments incorporating halogen atoms serve as promising starting points in hit-to-lead development as they often establish halogen bonds with target proteins, potentially enhancing binding affinity and selectivity, as well as counteracting drug resistance. Here, the aim was to unambiguously identify the binding orientations of fragment hits for SARS-CoV-2 nonstructural protein 1 (nsp1) which contain a combination of sulfur and/or chlorine, bromine and iodine substituents. The binding orientations of carefully selected nsp1 analogue hits were focused on by employing their anomalous scattering combined with Pan-Dataset Density Analysis (PanDDA). Anomalous difference Fourier maps derived from the diffraction data collected at both standard and long-wavelength X-rays were compared. The discrepancies observed in the maps of iodine-containing fragments collected at different energies were attributed to site-specific radiation-damage stemming from the strong X-ray absorption of I atoms, which is likely to cause cleavage of the C-I bond. A reliable and effective data-collection strategy to unambiguously determine the binding orientations of low-occupancy fragments containing sulfur and/or halogen atoms while mitigating radiation damage is presented.


  • Organizational Affiliation

    School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Host translation inhibitor nsp1118Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H0L (Subject of Investigation/LOI)
Query on A1H0L

Download Ideal Coordinates CCD File 
B [auth A]2-(1-benzothiophen-3-yl)ethanoic acid
C10 H8 O2 S
VFZQJKXVHYZXMM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.821α = 90
b = 36.821β = 90
c = 140.777γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release