6ACR

Crystal structure of human ALK2 kinase domain with R206H mutation in complex with RK-59638

• PDB DOI: https://doi.org/10.2210/pdb6ACR/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2018-07-27 Released: 2019-03-20 
• Deposition Author(s): Sakai, N., Mishima-Tsumagari, C., Matsumoto, T., Shirouzu, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.257 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 

Literature

Bis-Heteroaryl Pyrazoles: Identification of Orally Bioavailable Inhibitors of Activin Receptor-Like Kinase-2 (R206H).

Sekimata, K., Sato, T., Sakai, N., Watanabe, H., Mishima-Tsumagari, C., Taguri, T., Matsumoto, T., Fujii, Y., Handa, N., Honma, T., Tanaka, A., Shirouzu, M., Yokoyama, S., Miyazono, K., Hashizume, Y., Koyama, H.

(2019) Chem Pharm Bull (Tokyo) 67: 224-235

• PubMed: 30828000 
• DOI: https://doi.org/10.1248/cpb.c18-00598
• Primary Citation of Related Structures:  
  6ACR


• PubMed Abstract: 
  

  Mutant activin receptor-like kinase-2 (ALK2) was reported to be closely associated with the pathogenesis of fibrodysplasia ossificans progressiva (FOP) and diffuse intrinsic pontine glioma (DIPG), and therefore presents an attractive target for therapeutic intervention. Through in silico virtual screenings and structure-activity relationship studies assisted by X-ray crystallographic analyses, a novel series of bis-heteroaryl pyrazole was identified as potent inhibitors of ALK2 (R206H). Derived from in silico hit compound RK-59638 (6a), compound 18p was identified as a potent inhibitor of ALK2 (R206H) with good aqueous solubility, liver microsomal stability, and oral bioavailability.

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Organizational Affiliation: 

Drug Discovery Chemistry Platform Unit, RIKEN Center for Sustainable Resource Science.

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 70.33 kDa 
• Atom Count: 4,903 
• Modelled Residue Count: 587 
• Deposited Residue Count: 602 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Activin receptor type-1	A, B	301	Homo sapiens	Mutation(s): 1  Gene Names: ACVR1, ACVRLK2 EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for Q04771 (Homo sapiens) Explore Q04771  Go to UniProtKB:  Q04771
PHAROS:  Q04771 GTEx:  ENSG00000115170

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9TO	C [auth A], G [auth B]	N-(4-methoxyphenyl)-4-[3-(pyridin-3-yl)-1H-pyrazol-4-yl]pyrimidin-2-amine C19 H16 N6 O ANTWQGSNXAZMBT-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
9TO	Binding MOAD:  6ACR	IC50: 684 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.257 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.13	α = 90
b = 138.36	β = 90
c = 59.35	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-20 
Deposition Author(s): Sakai, N., Mishima-Tsumagari, C., Matsumoto, T., Shirouzu, M.

Revision History  

• Version 1.0: 2019-03-20
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description