9RXL | pdb_00009rxl

SARS-CoV-2 nucleocapsid C-terminal domain in complex with BCY00018176


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 
    0.214 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

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Ligand Structure Quality Assessment 


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Literature

Utilizing Constrained Bicyclic Peptides for In Vitro Diagnostics.

Shamsabadi, A.Creamer, A.Sadler, C.J.Abdelwahed, A.Gaynor, K.U.Demydchuk, Y.Ivanova-Berndt, G.Van Rietschoten, K.Beswick, P.Chen, L.Arruda Bezerra, G.Lulla, A.Brear, P.Hyvonen, M.Skynner, M.J.Stevens, M.M.

(2026) ACS Nano 

  • DOI: https://doi.org/10.1021/acsnano.5c19041
  • Primary Citation of Related Structures:  
    9RXL, 9S3N

  • PubMed Abstract: 

    Constrained bicyclic peptides ( Bicycle molecules ) with high affinity for biological targets have emerged as potentially powerful therapeutic agents, particularly for the in vivo targeting of cancer receptors. However, their antibody-mimetic properties have yet to be explored for use in diagnostic immunoassays. These synthetically derived compounds serve as biorecognition scaffolds that allow for facile site-selective modification and large-scale production. A phage display screen against various constructs of the SARS-CoV-2 nucleocapsid (N) protein identified several Bicycle molecules with binding affinities ranging from the micromolar to the low nanomolar range. These Bicycle molecules were validated in the development of enzyme- and nanozyme-linked immunosorbent assays, as well as enzymatic and colorimetric nanoparticle-based lateral flow immunoassays (LFIA) for the detection of ultralow concentrations of the SARS-CoV-2 N protein. We envision that these moieties enable robust, cost-effective, and large-scale development of ultrasensitive biosensors for a diverse range of biomarkers by leveraging their high binding affinity, minimalistic scaffold, and synthetic accessibility.


  • Organizational Affiliation
    • Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, U.K.

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BCY00018176
A, B
18Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoprotein
C, D
139Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC9 
Go to UniProtKB:  P0DTC9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free:  0.214 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.043α = 90
b = 73.043β = 90
c = 116.864γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-04
    Type: Initial release