9J9D | pdb_00009j9d

Crystal structure of ALK5 kinase domain in complex with inhibitor HM-279

• PDB DOI: https://doi.org/10.2210/pdb9J9D/pdb

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


• Deposited: 2024-08-22 Released: 2025-04-02 
• Deposition Author(s): Arai, M., Hanada, M., Taniguchi, H., Ohmoto, H., Naka, K., Sawa, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 
  0.209 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.200 (DCC) 

Starting Model: experimental

Literature

Discovery of HM-279, a Potent Inhibitor of ALK5 for Improving Therapeutic Efficacy of Cancer Immunotherapy.

Arai, M., Hanada, M., Taniguchi, H., Nakajima, F., Ohmoto, H., Inoue, T., Naka, K., Sawa, M.

(2025) J Med Chem 68: 7106-7118

• PubMed: 40108955 
• DOI: https://doi.org/10.1021/acs.jmedchem.4c02293
• Primary Citation of Related Structures:  
  9J9D


• PubMed Abstract: 
  

  Activin receptor-like kinase 5 (ALK5) is a type I receptor serine/threonine kinase and responsible for the TGF-β signaling pathway. ALK5 is thought to be a key player in the tumor microenvironment to promote tumor progression by affecting the anticancer immunity. Therefore, ALK5 is an attractive drug target for modulating TGF-β signaling pathways to improve the therapeutic efficacy of cancer immunotherapy. We report the optimization of a series of thiazole analogues starting from lead compound 6 , focusing on improving off-target selectivity. Compound 19f (HM-279) was identified as a potent ALK5 inhibitor with an acceptable off-target selectivity and favorable ADME/PK properties. Oral administration of HM-279 demonstrated antitumor activity in a CT26.WT colon carcinoma syngeneic mouse model as a single agent and in combination with the anti-PD-1 antibody through CD8 ⁺ T cell immunity.

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Organizational Affiliation: 
• Research and Development, Carna Biosciences, Inc., BMA 3F, 1-5-5 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
Graduate School of Pharmaceutical Sciences, Osaka University, Yamada-oka 1-6, Suita, Osaka 565-0871, Japan.
Department of Stem Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima 734-8553, Japan.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.65 kDa 
• Atom Count: 2,702 
• Modeled Residue Count: 296 
• 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
A1L30 (Subject of Investigation/LOI)	B [auth A]	2-((1-(but-2-yn-1-yl)-1H-pyrazol-4-yl)(cyclopropylmethyl)amino)-5-(4-(dimethylcarbamoyl)-1H-pyrrol-2-yl)thiazole-4-carboxamide C22 H25 N7 O2 S HACYEVIDLDLIII-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free:  0.209 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.200 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.455	α = 90
b = 75.677	β = 90
c = 89.625	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-02 
Deposition Author(s): Arai, M., Hanada, M., Taniguchi, H., Ohmoto, H., Naka, K., Sawa, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-04-02
  Type: Initial release
  
• Version 1.1: 2025-04-23
  Changes: Database references