8UWR

Crystal structure of human ACVR1 (ALK2) kinase in complex with compound 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

An ALK2 inhibitor, BLU-782, prevents heterotopic ossification in a mouse model of fibrodysplasia ossificans progressiva.

Davis, A.J.Brooijmans, N.Brubaker, J.D.Stevison, F.LaBranche, T.P.Albayya, F.Fleming, P.Hodous, B.L.Kim, J.L.Kim, S.Lobbardi, R.Palmer, M.Sheets, M.P.Vassiliadis, J.Wang, R.Williams, B.D.Wilson, D.Xu, L.Zhu, X.J.Bouchard, K.Hunter, J.W.Graul, C.Greenblatt, E.Hussein, A.Lyon, M.Russo, J.Stewart, R.Dorsch, M.Guzi, T.J.Kadambi, V.Lengauer, C.Garner, A.P.

(2024) Sci Transl Med 16: eabp8334-eabp8334

  • DOI: https://doi.org/10.1126/scitranslmed.abp8334
  • Primary Citation of Related Structures:  
    8UWN, 8UWR

  • PubMed Abstract: 

    Fibrodysplasia ossificans progressiva (FOP) is a rare genetic disease driven by gain-of-function variants in activin receptor-like kinase 2 (ALK2), the most common variant being ALK2 R206H . In FOP, ALK2 variants display increased and dysregulated signaling through the bone morphogenetic protein (BMP) pathway 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 BLU-782 (IPN60130), a small-molecule ALK2 R206H inhibitor developed for the treatment of FOP. A small-molecule library was screened in a biochemical ALK2 binding assay to identify potent ALK2 binding compounds. Iterative rounds of structure-guided drug design were used to optimize compounds for ALK2 R206H binding, ALK2 selectivity, and other desirable pharmacokinetic properties. BLU-782 preferentially bound to ALK2 R206H with high affinity, inhibiting signaling from ALK2 R206H and other rare FOP variants in cells in vitro without affecting signaling of closely related homologs ALK1, ALK3, and ALK6. In vivo efficacy of BLU-782 was demonstrated using a conditional knock-in ALK2 R206H mouse model, where prophylactic oral dosing reduced edema and prevented cartilage and heterotopic ossification (HO) in both muscle and bone injury models. BLU-782 treatment preserved the normal muscle-healing response in ALK2 R206H mice. Delayed dosing revealed a short 2-day window after injury when BLU-782 treatment prevented HO in ALK2 R206H mice, but dosing delays of 4 days or longer abrogated HO prevention. Together, these data suggest that BLU-782 may be a candidate for prevention of HO in FOP.


  • Organizational Affiliation

    Blueprint Medicines Corporation, Cambridge, MA 02139, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Activin receptor type-1323Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XQX (Subject of Investigation/LOI)
Query on XQX

Download Ideal Coordinates CCD File 
H [auth A]cyclopropyl(4-{(8R)-6-[4-(piperazin-1-yl)phenyl]pyrrolo[1,2-b]pyridazin-4-yl}piperazin-1-yl)methanone
C25 H30 N6 O
DCXFSRBQKGWSAK-UHFFFAOYSA-N
SO4
Query on SO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.61α = 90
b = 66.36β = 90
c = 162.14γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2024-11-06 
  • Deposition Author(s): Kim, J.L.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release