4BGG

Crystal structure of the ACVR1 kinase in complex with LDN-213844


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-Activity Relationship of 3,5-Diaryl-2-Aminopyridine Alk2 Inhibitors Reveals Unaltered Binding Affinity for Fibrodysplasia Ossificans Progressiva Causing Mutants.

Mohedas, A.H.Wang, Y.Sanvitale, C.E.Canning, P.Choi, S.Xing, X.Bullock, A.N.Cuny, G.D.Yu, P.B.

(2014) J.Med.Chem. 57: 7900

  • DOI: 10.1021/jm501177w

  • PubMed Abstract: 
  • There are currently no effective therapies for fibrodysplasia ossificans progressiva (FOP), a debilitating and progressive heterotopic ossification disease caused by activating mutations of ACVR1 encoding the BMP type I receptor kinase ALK2. Recently ...

    There are currently no effective therapies for fibrodysplasia ossificans progressiva (FOP), a debilitating and progressive heterotopic ossification disease caused by activating mutations of ACVR1 encoding the BMP type I receptor kinase ALK2. Recently, a subset of these same mutations of ACVR1 have been identified in diffuse intrinsic pontine glioma (DIPG) tumors. Here we describe the structure-activity relationship for a series of novel ALK2 inhibitors based on the 2-aminopyridine compound K02288. Several modifications increased potency in kinase, thermal shift, or cell-based assays of BMP signaling and transcription, as well as selectivity for ALK2 versus closely related BMP and TGF-β type I receptor kinases. Compounds in this series exhibited a wide range of in vitro cytotoxicity that was not correlated with potency or selectivity, suggesting mechanisms independent of BMP or TGF-β inhibition. The study also highlights a potent 2-methylpyridine derivative 10 (LDN-214117) with a high degree of selectivity for ALK2 and low cytotoxicity that could provide a template for preclinical development. Contrary to the notion that activating mutations of ALK2 might alter inhibitor efficacy due to potential conformational changes in the ATP-binding site, the compounds demonstrated consistent binding to a panel of mutant and wild-type ALK2 proteins. Thus, BMP inhibitors identified via activity against wild-type ALK2 signaling are likely to be of clinical relevance for the diverse ALK2 mutant proteins associated with FOP and DIPG.


    Organizational Affiliation

    Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACTIVIN RECEPTOR TYPE-1
A, B, C, D
301Homo sapiensMutation(s): 1 
Gene Names: ACVR1 (ACVRLK2)
EC: 2.7.11.30
Find proteins for Q04771 (Homo sapiens)
Go to Gene View: ACVR1
Go to UniProtKB:  Q04771
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FLC
Query on FLC

Download SDF File 
Download CCD File 
A, B, C
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
844
Query on 844

Download SDF File 
Download CCD File 
A, B, C, D
1-{4-[5-(3,4,5-trimethoxyphenyl)pyridin-3-yl]phenyl}piperazine
C24 H27 N3 O3
WFZZPLAPENBNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
844IC50: 15 - 250 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.215 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 85.380α = 90.00
b = 99.850β = 92.93
c = 187.438γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Database references