8ZBH | pdb_00008zbh

Crystal structure of TEAD3 YAP binding domain with compound 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.270 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Pan-Transcriptional Enhanced Associated Domain Palmitoylation Pocket Covalent Inhibitor.

Kim, J.Kim, H.Kim, J.Cho, S.Y.Moon, S.Yoo, Y.Kim, H.Kim, J.K.Jeon, H.Namkung, W.Han, G.No, K.T.

(2024) J Med Chem 67: 18957-18968

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01393
  • Primary Citation of Related Structures:  
    8ZBG, 8ZBH

  • PubMed Abstract: 

    In the Hippo signaling pathway, the palmitoylated transcriptional enhanced associated domain (TEAD) protein interacts with the coactivator Yes-associated protein/PDZ-binding motif, leading to transcriptional upregulation of oncogenes such as Ctgf and Cyr61. Consequently, targeting the palmitoylation sites of TEAD has emerged as a promising strategy for treating TEAD-dependent cancers. Compound 1 was identified using a structure-based drug design approach, leveraging the molecular insights gained from the known TEAD palmitoylation site inhibitor, K-975. Optimization of the initial hit compound resulted in the development of compound 3 , a covalent pan-TEAD inhibitor characterized by high potency and oral bioavailability.


  • Organizational Affiliation
    • The Interdisciplinary Graduate Program in Integrative Biotechnology & Translational Medicine, Yonsei University, Incheon 21983, 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
221Homo 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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.270 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.17α = 90
b = 101.74β = 90
c = 149.08γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
ELVESphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

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