9Q1M | pdb_00009q1m

Crystal structure of human TEAD2 Yap binding domain covalently bound to an allosteric regulator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.261 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9Q1M

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Small-Molecule Covalent Stabilization and Inhibition of the TEAD·YAP1 Transcription Factor in Cancer Cells.

Yeh, I.J.Bum-Erdene, K.Ghozayel, M.K.Gonzalez-Gutierrez, G.Meroueh, S.O.

(2025) ACS Chem Biol 20: 2142-2158

  • DOI: https://doi.org/10.1021/acschembio.5c00283
  • Primary Citation Related Structures: 
    9Q1M, 9Q1N, 9Q1O

  • PubMed Abstract: 

    Transcriptional enhanced associate domain transcription factors (TEAD1 to TEAD4) bind to transcriptional coactivator Yes-Associated Protein (YAP1) or its paralog transcriptional coactivator with PDZ-binding motif (TAZ) to regulate Hippo pathway target genes. The Hippo pathway is a conserved signaling pathway that regulates organ size and cell fate by controlling cell proliferation and apoptosis. Here we report small acrylamide molecules that form a covalent bond with a conserved cysteine at the TEAD palmitate pocket. Binding studies showed profound stabilization of TEADs by the small molecules, and cocrystal structures reveal that the compounds mimic the binding mode of palmitate. The small molecules achieved submicromolar binding constants and subhour reaction half-lives for all four TEADs. In mammalian cells, the compounds stabilize the TEAD•YAP1 interaction yet inhibit the TEAD transcription factor activity. Unexpectedly, several compounds degraded TEAD and YAP1 proteins and inhibited cancer cell viability. This work suggests that degradation of TEAD and YAP1 may amplify the antitumor effects of small molecules targeting the TEAD palmitate pocket, with implications for other cancer targets featuring allosteric lipid-binding sites.


  • Organizational Affiliation
    • Department of Veterans Affairs, Richard L. Roudebush VA Medical Center, Indianapolis, Indiana 46202, United States.

Macromolecule Content 

  • Total Structure Weight: 53.92 kDa 
  • Atom Count: 3,355 
  • Modeled Residue Count: 398 
  • Deposited Residue Count: 468 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcriptional enhancer factor TEF-4A [auth B],
B [auth A]
234Homo sapiensMutation(s): 0 
Gene Names: TEAD2TEF4
UniProt & NIH Common Fund Data Resources
Find proteins for Q15562 (Homo sapiens)
Explore Q15562 
Go to UniProtKB:  Q15562
PHAROS:  Q15562
GTEx:  ENSG00000074219 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15562
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.261 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.298α = 90
b = 60.805β = 111.53
c = 80.057γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited StatesP30CA082709
Other privateUnited StatesVera Bradley Foundation

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2025-10-01
    Changes: Database references
  • Version 1.2: 2026-03-04
    Changes: Refinement description