Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.61 kDa 
• Atom Count: 2558 
• Modelled Residue Count: 295 
• Deposited Residue Count: 309 
• Unique protein chains: 1

3TZM

TGF-beta Receptor type 1 in complex with SB431542

• PDB DOI: 10.2210/pdb3TZM/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-09-27 Released: 2012-05-23 
• Deposition Author(s): Ogunjimi, A.A., Zeqiraj, E., Ceccarelli, D.F., Sicheri, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.205 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Literature

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

• PubMed: 21983015 
• DOI: 10.1016/j.cellsig.2011.09.027
• Primary Citation of Related Structures:  
  3TZM


• 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.

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Organizational Affiliation: 

Center for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TGF-beta receptor type-1	A	309	Homo sapiens	Mutation(s): 0  Gene Names: TGFBR1, ALK5, SKR4 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
085	B [auth A]	4-[5-(1,3-benzodioxol-5-yl)-4-(pyridin-2-yl)-1H-imidazol-2-yl]benzamide C22 H16 N4 O3 FHYUGAJXYORMHI-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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

• Method: X-RAY DIFFRACTION
• 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 = 41.771	α = 90
b = 77.726	β = 90
c = 90.07	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-09-27 
• Released Date: 2012-05-23 
Deposition Author(s): Ogunjimi, A.A., Zeqiraj, E., Ceccarelli, D.F., Sicheri, F.

Revision History  

• Version 1.0: 2012-05-23
  Type: Initial release