TGF-beta Receptor type 1 in complex with SB431542

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

Starting Model: experimental
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Structural Basis for Specificity of TGFbeta Family Receptor Small Molecule Inhibitors

Ogunjimi, A.A.Zeqiraj, E.Ceccarelli, D.F.Sicheri, F.Wrana, J.L.David, L.

(2012) Cell Signal 24: 476-483

  • DOI: https://doi.org/10.1016/j.cellsig.2011.09.027
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Transforming growth factor-β (TGFβ) receptor kinase inhibitors have a great therapeutic potential. SB431542 is one of the mainly used kinase inhibitors of the TGFβ/Activin pathway receptors, but needs improvement of its EC(50) (EC(50)=1 μM) to be translated to clinical use. A key feature of SB431542 is that it specifically targets receptors from the TGFβ/Activin pathway but not the closely related receptors from the bone morphogenic proteins (BMP) pathway. To understand the mechanisms of this selectivity, we solved the crystal structure of the TGFβ type I receptor (TβRI) kinase domain in complex with SB431542. We mutated TβRI residues coordinating SB431542 to their counterparts in activin-receptor like kinase 2 (ALK2), a BMP receptor kinase, and tested the kinase activity of mutated TβRI. We discovered that a Ser280Thr mutation yielded a TβRI variant that was resistant to SB431542 inhibition. Furthermore, the corresponding Thr283Ser mutation in ALK2 yielded a BMP receptor sensitive to SB431542. This demonstrated that Ser280 is the key determinant of selectivity for SB431542. This work provides a framework for optimising the SB431542 scaffold to more potent and selective inhibitors of the TGFβ/Activin pathway.

  • Organizational Affiliation

    Center for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TGF-beta receptor type-1309Homo sapiensMutation(s): 0 
Gene Names: TGFBR1ALK5SKR4
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
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 085

Download Ideal Coordinates CCD File 
B [auth A]4-[5-(1,3-benzodioxol-5-yl)-4-(pyridin-2-yl)-1H-imidazol-2-yl]benzamide
C22 H16 N4 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
085 BindingDB:  3TZM Ki: 17 (nM) from 1 assay(s)
Kd: 190 (nM) from 1 assay(s)
IC50: min: 66, max: 1542 (nM) from 8 assay(s)
EC50: 172 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.771α = 90
b = 77.726β = 90
c = 90.07γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description