9HF4 | pdb_00009hf4

Crystal structure of human TRF1 TRFH domain in complex with compound 32


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 
    0.258 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Model: experimental
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Literature

Discovery of first-in-class inhibitors of the TRF1:TIN2 protein:protein interaction by fragment screening.

Casale, G.Liu, M.Le Bihan, Y.V.Inian, O.Stammers, E.Caldwell, J.van Montfort, R.L.M.Collins, I.Guettler, S.

(2025) Sci Rep 15: 40922-40922

  • DOI: https://doi.org/10.1038/s41598-025-23858-3
  • Primary Citation of Related Structures:  
    9HCL, 9HCM, 9HCN, 9HCP, 9HCQ, 9HCR, 9HCS, 9HCT, 9HCU, 9HCV, 9HCW, 9HCX, 9HCY, 9HCZ, 9HD0, 9HD1, 9HD2, 9HD3, 9HD9, 9HDA, 9HF4, 9HF6, 9HF7, 9HF8, 9HF9, 9HFA, 9HFB, 9HFC, 9HFD, 9HFE, 9HFF, 9HFG, 9HFH, 9HFI, 9HHK, 9HLP, 9HLQ, 9HLR, 9HLT, 9HLU

  • PubMed Abstract: 

    TRF1 is a subunit of the shelterin complex that binds to and protects the linear ends of chromosomes known as telomeres. Both genetic deletion and chemical inhibition of TRF1 have been shown to block the growth of lung carcinoma, glioblastoma, and renal cell carcinoma in mice without affecting mouse survival or tissue function, making TRF1 a potential therapeutic target in cancer 1-3 . Here, we report the discovery of a series of fragment hits that bind at the interface between the TRFH domain of TRF1 (TRF1 TRFH ) and a peptide of TIN2 (TIN2 TBM ), an interaction essential for the recruitment of TRF1 to shelterin, using X-ray crystallography (XChem) and ligand-observed NMR (LO-NMR) fragment screening. We discovered a first-in-class inhibitor of the TRF1:TIN2 interaction (compound 40) that binds to TRF1 TRFH with a K D of 29 µM (95% CI: 20-41 µM), displaces a TIN2 probe with an IC 50 of 67 µM (95% CI: 10-120 µM), and expels TRF1 from purified shelterin. Aided by a novel crystal system of TRF1 TRFH , we characterised fragments binding in a hotspot at the TRF1:TIN2 interface; these will serve as a starting point for the structure-guided development of potent inhibitors of TRF1 protein:protein interactions to disrupt shelterin complex assembly.


  • Organizational Affiliation
    • Division of Structural Biology, The Institute of Cancer Research (ICR), London, SW7 3RP, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Telomeric repeat-binding factor 1224Homo sapiensMutation(s): 0 
Gene Names: TERF1PIN2TRBF1TRFTRF1
UniProt & NIH Common Fund Data Resources
Find proteins for P54274 (Homo sapiens)
Explore P54274 
Go to UniProtKB:  P54274
PHAROS:  P54274
GTEx:  ENSG00000147601 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54274
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IUC (Subject of Investigation/LOI)
Query on A1IUC

Download Ideal Coordinates CCD File 
B [auth A]4-phenylmethoxynaphthalene-1-sulfonic acid
C17 H14 O4 S
ZYIBEMACOFTWFX-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
C [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free:  0.258 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.726α = 90
b = 51.726β = 90
c = 145.241γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom214311/Z/18/Z

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Database references