Crystal structure of TGFbRI complexed with an indolinone inhibitor

Experimental Data Snapshot

  • Resolution: 3.70 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.267 

Starting Model: experimental
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Design, Synthesis and Evaluation of Indolinones as Inhibitors of the Transforming Growth Factor Beta Receptor I (Tgfbri)

Roth, G.J.Heckel, A.Brandl, T.Grauert, M.Hoerer, S.Kley, J.T.Schnapp, G.Baum, P.Mennerich, D.Schnapp, A.Park, J.E.

(2010) J Med Chem 53: 7287

  • DOI: https://doi.org/10.1021/jm100812a
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Inhibition of transforming growth factor β (TGFβ) type I receptor (Alk5) offers a novel approach for the treatment of fibrotic diseases and cancer. Indolinones substituted in position 6 were identified as a new chemotype inhibiting TGFβRI concomitant with a low cross-reactivity among the human kinome. A subset of compounds showed additional inhibition of platelet-derived growth factor receptor alpha (PDGFRα), contributing to an interesting pharmacological profile. In contrast, p38 kinase, which is often inhibited by TGFβRI inhibitors, was not targeted by derivatives based on the indolinone chemotype. Guided by an X-ray structure of lead compound 5 (BIBF0775) soaked into the kinase domain of TGFβRI, optimization furnished potent and selective inhibitors of TGFβRI. Potent inhibition translated well into good inhibition of TGFβRI-mediated phosphorylation of Smad2/3, demonstrating efficacy in a cellular setting. Optimized compounds were extensively profiled on a 232-kinase panel and showed low cross-reactivities within the human kinome.

  • Organizational Affiliation

    Biberach, Department of Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Strasse 65,D-88397 Biberach, Germany. gerald.roth@boehringer-ingelheim.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
342Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P36897 (Homo sapiens)
Explore P36897 
Go to UniProtKB:  P36897
GTEx:  ENSG00000106799 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36897
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
ZOP PDBBind:  2X7O IC50: 34 (nM) from 1 assay(s)
BindingDB:  2X7O IC50: 34 (nM) from 1 assay(s)
EC50: 105 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.70 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.267 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.929α = 90
b = 246.561β = 90
c = 131.617γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-20
    Type: Initial release
  • Version 1.1: 2011-05-19
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-04-03
    Changes: Data collection, Other, Source and taxonomy
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description