9R5Y | pdb_00009r5y

Crystal structure of the C-terminal domain of human TNC in complex with Adhiron 52


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.185 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.160 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Targeting Tenascin-C-Toll-like Receptor 4 signalling with Adhiron-derived small molecules - a viable strategy for reducing fibrosis in systemic sclerosis.

Gaule, T.Simmons, K.J.Walker, K.Del Galdo, F.Ross, R.L.Viswambharan, H.Krishnappa, J.Pacey, J.McPhillie, M.Tomlinson, D.C.Maqbool, A.

(2025) Bioorg Chem 167: 109251-109251

  • DOI: https://doi.org/10.1016/j.bioorg.2025.109251
  • Primary Citation of Related Structures:  
    9R5Y

  • PubMed Abstract: 

    Tissue fibrosis is a hallmark of systemic sclerosis (SSc) and results from the persistent activation of fibroblasts and excessive accumulation of extracellular matrix component such as collagen. Recent evidence implicates the matricellular protein Tenascin-C (TNC) in promoting self-sustaining fibroblast activation and fibrosis via its interaction with Toll-like receptor 4 (TLR4). In this study, we utilized Adhiron-guided ligand discovery to identify small molecule inhibitors targeting the fibrinogen-like globe domain of TNC, a key mediator of TLR4 activation. Two lead compounds (464 and 830) demonstrated structural similarity, favourable ADME profiles, and robust anti-fibrotic activity in vitro. Treatment of dermal fibroblasts derived from SSc patients with either compound significantly reduced Transforming growth factor-β-induced expression of fibrotic genes, ACTA2, COL1A1, COL1A2, and CCN2, and inhibited myofibroblast differentiation. These studies may facilitate the development of effective targeted therapy for fibrosis in SSc and support this novel strategy for small molecule development.


  • Organizational Affiliation
    • Clinical Population and Sciences Department, Leeds Institute for Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, United Kingdom.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tenascin
A, D
219Homo sapiensMutation(s): 1 
Gene Names: TNCHXB
UniProt & NIH Common Fund Data Resources
Find proteins for P24821 (Homo sapiens)
Explore P24821 
Go to UniProtKB:  P24821
PHAROS:  P24821
GTEx:  ENSG00000041982 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24821
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Adhiron
B, C
88synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.185 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.160 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.535α = 90
b = 90.152β = 90
c = 104.409γ = 90
Software Package:
Software NamePurpose
xia2data reduction
PHASERphasing
Cootmodel building
REFMACrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
British Heart FoundationUnited KingdomPG/17/72/33255

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Database references