8ZBG | pdb_00008zbg

Crystal structure of TEAD3 YAP binding domain with compound 15

• PDB DOI: https://doi.org/10.2210/pdb8ZBG/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-26 Released: 2025-04-16 
• Deposition Author(s): Yoo, Y., Kim, H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 
  0.261 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

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

• PubMed: 39487823 
• DOI: https://doi.org/10.1021/acs.jmedchem.4c01393
• Primary Citation 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.

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Organizational Affiliation: 
• The Interdisciplinary Graduate Program in Integrative Biotechnology & Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea.
Baobab AiBIO Co., Ltd., Incheon 21983, Republic of Korea.
Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Republic of Korea.
Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.
Department of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea.
Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea.
Postech Biotech Center, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea.
Institute of Convergence Science and Technology, Yonsei University, Incheon 21983, Republic of Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 77.24 kDa 
• Atom Count: 5,458 
• Modeled Residue Count: 661 
• Deposited Residue Count: 663 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional enhancer factor TEF-5	A, B, C	221	Homo sapiens	Mutation(s): 0  Gene Names: TEAD3, TEAD5, TEF5
UniProt & NIH Common Fund Data Resources
Find proteins for Q99594 (Homo sapiens) Explore Q99594  Go to UniProtKB:  Q99594
PHAROS:  Q99594 GTEx:  ENSG00000007866

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L1N (Subject of Investigation/LOI)	D [auth A], E [auth B], F [auth C]	(2~{R})-2-fluoranyl-1-[7-[4-(trifluoromethyl)phenyl]-3,4-dihydro-1~{H}-isoquinolin-2-yl]propan-1-one C19 H17 F4 N O SBGBAMLYHBLWPL-GFCCVEGCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free:  0.261 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.23	α = 90
b = 101.16	β = 90
c = 148.85	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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