6E5G | pdb_00006e5g

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 
    0.268 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Small-Molecule Covalent Modification of Conserved Cysteine Leads to Allosteric Inhibition of the TEAD⋅Yap Protein-Protein Interaction.

Bum-Erdene, K.Zhou, D.Gonzalez-Gutierrez, G.Ghozayel, M.K.Si, Y.Xu, D.Shannon, H.E.Bailey, B.J.Corson, T.W.Pollok, K.E.Wells, C.D.Meroueh, S.O.

(2019) Cell Chem Biol 26: 378

  • DOI: https://doi.org/10.1016/j.chembiol.2018.11.010
  • Primary Citation Related Structures: 
    6E5G

  • PubMed Abstract: 

    The Hippo pathway coordinates extracellular signals onto the control of tissue homeostasis and organ size. Hippo signaling primarily regulates the ability of Yap1 to bind and co-activate TEA domain (TEAD) transcription factors. Yap1 tightly binds to TEAD4 via a large flat interface, making the development of small-molecule orthosteric inhibitors highly challenging. Here, we report small-molecule TEAD⋅Yap inhibitors that rapidly and selectively form a covalent bond with a conserved cysteine located within the unique deep hydrophobic palmitate-binding pocket of TEADs. Inhibition of TEAD4 binding to Yap1 by these compounds was irreversible and occurred on a longer time scale. In mammalian cells, the compounds formed a covalent complex with TEAD4, inhibited its binding to Yap1, blocked its transcriptional activity, and suppressed expression of connective tissue growth factor. The compounds inhibited cell viability of patient-derived glioblastoma spheroids, making them suitable as chemical probes to explore Hippo signaling in cancer.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.

Macromolecule Content 

  • Total Structure Weight: 53.99 kDa 
  • Atom Count: 3,515 
  • Modeled Residue Count: 415 
  • Deposited Residue Count: 470 
  • 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]
235Homo 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
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free:  0.268 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.757α = 90
b = 61.226β = 116.89
c = 79.839γ = 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


Funding OrganizationLocationGrant Number
American Cancer SocietyUnited StatesRSG-12-092-01-CDD

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-09
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary