9L04 | pdb_00009l04

Crystal structure of human ALK2 kinase domain with R206H mutation in complex with RK783


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.256 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

A new BMP type 1 receptor kinase inhibitor for safe and efficient oral treatment to prevent genetically induced heterotopic ossification in mice.

Yang, J.Pan, H.Sekimata, K.Hwang, C.Kulkarni, A.Thomas, H.Lindenau, J.Duford, T.Ueharu, H.Tanaka, A.Sakai, N.Shirouzu, M.Hashizume, Y.Levi, B.Koyama, H.Mishina, Y.

(2025) Bone : 117565-117565

  • DOI: https://doi.org/10.1016/j.bone.2025.117565
  • Primary Citation of Related Structures:  
    9L04

  • PubMed Abstract: 

    Fibrodysplasia ossificans progressiva (FOP) is a rare genetic heterotopic ossification (HO) disorder that currently lacks a practical and definitive preventative approach. FOP is driven by gain-of-function variants in ACVR1, increasing dysregulated BMP signaling pathway, thus resulting in progressive and permanent replacement of skeletal muscle and connective tissues with heterotopic bone, ultimately leading to severe debilitation and premature death. Here, we describe the discovery of RK783, a small-molecule that inhibit BMP type 1 receptor kinase developed for treating FOP. This compound, the result of a rigorous process that involved screening approximately 140,000 compounds in silico with ligand-based structure followed by inhibitory activity and pharmacokinetics studies, offers a promising new direction in treating FOP. RK783 preferentially suppressed both basal and stimulated BMP-Smad1/5/9 signaling in vitro without affecting the signaling of Smad2/3. In vivo, the efficacy of RK783 was demonstrated using two FOP mice models, a conditional knock-in ACVR1-R206H and a transgenic ACVR1-Q207D mouse model, where oral dosing suppressed infiltration of immune cells and differentiation of fibroblast-adipose progenitor (FAP) cells, thus preventing ectopic cartilage and HO formation in muscles. Optimized dosing revealed that high and frequent treatment within the first couple of days after HO induction is critical to successfully suppress HO by RK738. These data suggest that RK783 can be used as an acute medication to prevent HO in FOP.


  • Organizational Affiliation
    • State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China.; Department of Biologic and Materials Sciences & Prosthodontics, University of Michigan School of Dentistry, 1010 N. University Ave, Ann Arbor, MI, 48179, USA. Electronic address: jingwen.yang@whu.edu.cn.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Activin receptor type-1301Homo sapiensMutation(s): 1 
Gene Names: ACVR1ACVRLK2
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04771
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L4C (Subject of Investigation/LOI)
Query on A1L4C

Download Ideal Coordinates CCD File 
B [auth A]4-(1-ethyl-3-pyridin-3-yl-pyrazol-4-yl)-~{N}-[4-[4-(oxetan-3-yl)piperazin-1-yl]phenyl]pyrimidin-2-amine
C27 H30 N8 O
WDBAIPMUEUJXOZ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.256 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.037α = 90
b = 86.424β = 90
c = 140.098γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release