9F6X | pdb_00009f6x

Human transforming growth factor b type I receptor in complex with kinase inhibitor SB505124

• PDB DOI: https://doi.org/10.2210/pdb9F6X/pdb

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


• Deposited: 2024-05-02 Released: 2024-12-25 
• Deposition Author(s): Rodriguez Buitrago, J.A., Landstrom, M., Wolf-Watz, M.
• Funding Organization(s): Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 
  0.248 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Human transforming growth factor beta type I receptor in complex with kinase inhibitor SB505124.

Rodriguez Buitrago, J.A., Landstrom, M., Wolf-Watz, M.

(2024) Acta Crystallogr F Struct Biol Commun 80: 314-319

• PubMed: 39441620 
• DOI: https://doi.org/10.1107/S2053230X24010094
• Primary Citation of Related Structures:  
  9F6X


• PubMed Abstract: 
  

  The crystal structure of the intracellular domain of transforming growth factor β type I receptor (TβR1) in complex with the competitive inhibitor SB505124 is presented. The study provides insights into the structure and function of TβR1 in complex with SB505124, and as such offers molecular-level understanding of the inhibition of this critical signalling pathway. The potential of SB505124 as an avenue for therapy in cancer treatment is discussed on basis of the results.

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Organizational Affiliation: 
• Department of Chemistry, Umeå University, Linnaeus vag 10, 901 87 Umeå, Sweden.
Department of Medical Biosciences, Umeå University, 901 85 Umeå, Sweden.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.09 kDa 
• Atom Count: 2,555 
• Modeled Residue Count: 303 
• Deposited Residue Count: 303 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TGF-beta receptor type-1	A	303	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 GTEx:  ENSG00000106799

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IAZ (Subject of Investigation/LOI)	B [auth A]	2-[5-(1,3-benzodioxol-5-yl)-2-~{tert}-butyl-1~{H}-imidazol-4-yl]-6-methyl-pyridine C20 H21 N3 O2 WGZOTBUYUFBEPZ-UHFFFAOYSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free:  0.248 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.07	α = 90
b = 79.846	β = 90
c = 87.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
STARANISO	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-25 
Deposition Author(s): Rodriguez Buitrago, J.A., Landstrom, M., Wolf-Watz, M.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	FS 506-21
Swedish Research Council	Sweden	2021-04513_VR

Revision History  

• Version 1.0: 2024-12-25
  Type: Initial release