9IXT | pdb_00009ixt

Crystal structure of TEAD3 YAP binding domain with compound 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.249 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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Literature

Structure-based optimization of TEAD inhibitors: Exploring a novel subpocket near Glu347 for the treatment of NF2-mutant cancer.

Kim, J.K.Kim, J.Kim, H.Jin, H.Yoo, Y.Fei, X.Maeng, H.J.Seo, S.Y.Han, G.No, K.T.

(2025) Bioorg Chem 159: 108425-108425

  • DOI: https://doi.org/10.1016/j.bioorg.2025.108425
  • Primary Citation of Related Structures:  
    9IXS, 9IXT

  • PubMed Abstract: 

    The Hippo signaling pathway is critical for regulating cell growth, tissue homeostasis, and organ size. Dysregulation of this pathway has been associated with a range of pathologies, especially cancer, through its modulation of downstream effectors-Yes-associated protein (YAP) and the transcriptional coactivator with PDZ-binding motif (TAZ). These proteins bind to transcriptional enhanced associate domain (TEAD) proteins and function as transcription factors in the nucleus, producing oncogenic target genes such as CTGF and CYR61. TEAD proteins require palmitoylation via a covalent bond with cysteine in the central pocket to bind YAP/TAZ. Therefore, competitive inhibition that prevents palmitoylation could serve as an effective anticancer strategy. In this study, we analyzed the crystal structures of the known inhibitor VT-105 bound to TEAD3 to identify new binding spots that were previously unexplored, with the aim of discovering more potent compounds using structure-based drug design. Consequently, we identified a novel hydrogen-bonding site and discovered C-2, which effectively binds to this site, as confirmed by X-ray crystallography. Furthermore, C-2 exhibited stable pharmacokinetic properties and demonstrated impressive efficacy in a mouse xenograft model.


  • Organizational Affiliation
    • Baobab AiBIO Co., Ltd., Incheon 21983, Republic of Korea; Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University, Incheon 21936, Republic of Korea.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional enhancer factor TEF-5
A, B, C
222Homo sapiensMutation(s): 0 
Gene Names: TEAD3TEAD5TEF5
UniProt & NIH Common Fund Data Resources
Find proteins for Q99594 (Homo sapiens)
Explore Q99594 
Go to UniProtKB:  Q99594
PHAROS:  Q99594
GTEx:  ENSG00000007866 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99594
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.249 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.18α = 90
b = 102.61β = 90
c = 148.71γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-04-16 
  • Deposition Author(s): Yoo, Y.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release