5QIM

TGF-BETA RECEPTOR TYPE 1 KINASE DOMAIN (T204D) IN COMPLEX WITH N-{4-[3-(5-METHOXYPYRIDIN-2-YL)-1H-PYRROLO[3,2-B] PYRIDIN-2-YL]PYRIDIN-2-YL}ACETAMIDE

• PDB DOI: https://doi.org/10.2210/pdb5QIM/pdb
• Deposition Group: G_1002052 ExploreG_1002052

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


• Deposited: 2018-08-05 Released: 2018-10-31 
• Deposition Author(s): Sheriff, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.188 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 

Literature

Discovery of 4-Azaindole Inhibitors of TGF beta RI as Immuno-oncology Agents.

Zhang, Y., Zhao, Y., Tebben, A.J., Sheriff, S., Ruzanov, M., Fereshteh, M.P., Fan, Y., Lippy, J., Swanson, J., Ho, C.P., Wautlet, B.S., Rose, A., Parrish, K., Yang, Z., Donnell, A.F., Zhang, L., Fink, B.E., Vite, G.D., Augustine-Rauch, K., Fargnoli, J., Borzilleri, R.M.

(2018) ACS Med Chem Lett 9: 1117-1122

• PubMed: 30429955 
• DOI: https://doi.org/10.1021/acsmedchemlett.8b00357
• Primary Citation of Related Structures:  
  5QIK, 5QIL, 5QIM, 5QIN


• PubMed Abstract: 
  

  The multifunctional cytokine TGFβ plays a central role in regulating antitumor immunity. It has been postulated that inhibition of TGFβ signaling in concert with checkpoint blockade will provide improved and durable immune response against tumors. Herein, we describe a novel series of 4-azaindole TGFβ receptor kinase inhibitors with excellent selectivity for TGFβ receptor 1 kinase. The combination of compound 3f and an antimouse-PD-1 antibody demonstrated significantly improved antitumor efficacy compared to either treatment alone in a murine tumor model.

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Organizational Affiliation: 

Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, New Jersey 08543, United States.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 35.39 kDa 
• Atom Count: 2,645 
• Modelled Residue Count: 304 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TGF-beta receptor type-1	A	306	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
J2Y	B [auth A]	N-{4-[3-(5-methoxypyridin-2-yl)-1H-pyrrolo[3,2-b]pyridin-2-yl]pyridin-2-yl}acetamide C20 H17 N5 O2 VRPRBQAJAQCSCW-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
J2Y	BindingDB:  5QIM	IC50: 6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.188 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.01	α = 90
b = 77.8	β = 90
c = 90.27	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
AMoRE	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-31 
Deposition Author(s): Sheriff, S.

Revision History  

• Version 1.0: 2018-10-31
  Type: Initial release
  
• Version 1.1: 2018-12-26
  Changes: Data collection, Database references
• Version 1.2: 2021-05-12
  Changes: Structure summary
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references