9GAX | pdb_00009gax

TEAD1 in complex with a reversible inhibitor N-[(1S)-2-hydroxy-1-(1-methyl-1H-pyrazol-3-yl)ethyl]-2-methyl-8-[4-(trifluoromethyl)phenyl]-2H,8H-pyrazolo[3,4-b]indole-5-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 
    0.219 (Depositor) 
  • R-Value Work: 
    0.186 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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Literature

MoA Studies of the TEAD P-Site Binding Ligand MSC-4106 and Its Optimization to TEAD1-Selective Amide M3686.

Heinrich, T.Schwarz, D.Petersson, C.Gunera, J.Garg, S.Schneider, R.Keil, M.Grimmeisen, L.Unzue Lopez, A.Albers, L.Schlesiger, S.Gambardella, A.Bomke, J.Carswell, E.Schilke, H.Diehl, P.Doerfel, B.Musil, D.Trivier, E.Broome, R.Marshall, S.Balsiger, A.Friedrich, E.Lemos, A.R.Santos, S.P.Sousa, P.M.F.Freire, F.Bandeiras, T.M.Bortoluzzi, A.Wienke, D.

(2025) J Med Chem 68: 6149-6164

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01949
  • Primary Citation of Related Structures:  
    9GAX

  • PubMed Abstract: 

    Taking the structural information into account, we were able to tune the TEAD selectivity for a specific chemotype. However, different TEAD selectivity profiles did not affect the compound potency or efficacy in the NCI-H226 viability assay. Amides based on MSC-4106 or analogues showed improved viability efficacy compared with the corresponding acids. The amide M3686 exhibited AUC-driven efficacy in NCI-H226 xenograft models and had an improved 25-fold lower human dose prediction than MSC-4106 . MSC-4106 was also used in HDX-MS studies to aid in the understanding of the MoA of P-site binding TEAD inhibitors. Artificial P-site binders rigidify certain areas in the periphery of the transcription factor that seem to be crucial for cofactor interaction, whereas a native fatty acid increased the protein dynamics of cofactor-binding interfaces.


  • Organizational Affiliation
    • Merck Healthcare KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional enhancer factor TEF-1
A, B
220Homo sapiensMutation(s): 0 
Gene Names: TEAD1TCF13TEF1
UniProt & NIH Common Fund Data Resources
Find proteins for P28347 (Homo sapiens)
Explore P28347 
Go to UniProtKB:  P28347
PHAROS:  P28347
GTEx:  ENSG00000187079 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28347
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IJL (Subject of Investigation/LOI)
Query on A1IJL

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
2-methyl-~{N}-[(1~{S})-1-(1-methylpyrazol-3-yl)-2-oxidanyl-ethyl]-4-[4-(trifluoromethyl)phenyl]pyrazolo[3,4-b]indole-7-carboxamide
C24 H21 F3 N6 O2
OQLMDCHCWZTHBV-HXUWFJFHSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
J [auth B]
K [auth B]
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free:  0.219 (Depositor) 
  • R-Value Work:  0.186 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.995α = 90
b = 107.995β = 90
c = 132.202γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
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: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Database references