8CAA

Crystal structure of TEAD4 in complex with YTP-13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Optimization of a Class of Dihydrobenzofurane Analogs toward Orally Efficacious YAP-TEAD Protein-Protein Interaction Inhibitors.

Sellner, H.Chapeau, E.Furet, P.Voegtle, M.Salem, B.Le Douget, M.Bordas, V.Groell, J.M.Le Goff, A.L.Rouzet, C.Wietlisbach, T.Zimmermann, T.McKenna, J.Brocklehurst, C.E.Chene, P.Wartmann, M.Scheufler, C.Kallen, J.Williams, G.Harlfinger, S.Traebert, M.Dumotier, B.M.Schmelzle, T.Soldermann, N.

(2023) ChemMedChem 18: e202300051-e202300051

  • DOI: https://doi.org/10.1002/cmdc.202300051
  • Primary Citation of Related Structures:  
    8CAA

  • PubMed Abstract: 

    The inhibition of the YAP-TEAD protein-protein interaction constitutes a promising therapeutic approach for the treatment of cancers linked to the dysregulation of the Hippo signaling pathway. The identification of a class of small molecules which potently inhibit the YAP-TEAD interaction by binding tightly to the Ω-loop pocket of TEAD has previously been communicated. This report details the further multi-parameter optimization of this class of compounds resulting in advanced analogs combining nanomolar cellular potency with a balanced ADME and off-target profile, and efficacy of these compounds in tumor bearing mice is demonstrated for the first time.


  • Organizational Affiliation

    Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional enhancer factor TEF-3
A, B
220Homo sapiensMutation(s): 0 
Gene Names: TEAD4RTEF1TCF13L1TEF3
UniProt & NIH Common Fund Data Resources
Find proteins for Q15561 (Homo sapiens)
Explore Q15561 
Go to UniProtKB:  Q15561
PHAROS:  Q15561
GTEx:  ENSG00000197905 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15561
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U3F (Subject of Investigation/LOI)
Query on U3F

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
4-[bis(fluoranyl)methoxy]-2-[(2~{S})-5-chloranyl-6-fluoranyl-2-[[(4-oxidanylcyclohexyl)amino]methyl]-2-phenyl-3~{H}-1-benzofuran-4-yl]-3-fluoranyl-benzamide
C29 H27 Cl F4 N2 O4
FXFZYILRQQAUGE-RIYSCVPDSA-N
U3O
Query on U3O

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
(2~{R})-2-[2-chloranyl-5-[2-chloranyl-4-(trifluoromethyl)phenoxy]phenyl]sulfanylpropanoic acid
C16 H11 Cl2 F3 O3 S
NFVBERYRRKUMCL-MRVPVSSYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.729α = 90
b = 89.397β = 90
c = 135.473γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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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: 2023-04-12
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection