2X7O | pdb_00002x7o

Crystal structure of TGFbRI complexed with an indolinone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 
    0.273 (Depositor), 0.317 (DCC) 
  • R-Value Work: 
    0.267 (Depositor), 0.318 (DCC) 
  • R-Value Observed: 
    0.267 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

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 Related Structures: 
    2X7O

  • 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

Macromolecule Content 

  • Total Structure Weight: 197.08 kDa 
  • Atom Count: 13,330 
  • Modeled Residue Count: 1,650 
  • Deposited Residue Count: 1,710 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TGF-BETA RECEPTOR TYPE I
A, B, C, D, E
342Homo sapiensMutation(s): 0 
EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for P36897 (Homo sapiens)
Explore P36897 
Go to UniProtKB:  P36897
PHAROS:  P36897
GTEx:  ENSG00000106799 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36897
Sequence Annotations
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
ZOP BindingDB:  2X7O IC50: 34 (nM) from 1 assay(s)
EC50: 105 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free:  0.273 (Depositor), 0.317 (DCC) 
  • R-Value Work:  0.267 (Depositor), 0.318 (DCC) 
  • R-Value Observed: 0.267 (Depositor) 
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
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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