3Q4U

Crystal structure of the ACVR1 kinase domain in complex with LDN-193189


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A new class of small molecule inhibitor of BMP signaling.

Sanvitale, C.E.Kerr, G.Chaikuad, A.Ramel, M.C.Mohedas, A.H.Reichert, S.Wang, Y.Triffitt, J.T.Cuny, G.D.Yu, P.B.Hill, C.S.Bullock, A.N.

(2013) PLoS One 8: e62721-e62721

  • DOI: 10.1371/journal.pone.0062721
  • Primary Citation of Related Structures:  
    3MTF, 3Q4U

  • PubMed Abstract: 
  • Growth factor signaling pathways are tightly regulated by phosphorylation and include many important kinase targets of interest for drug discovery. Small molecule inhibitors of the bone morphogenetic protein (BMP) receptor kinase ALK2 (ACVR1) are needed urgently to treat the progressively debilitating musculoskeletal disease fibrodysplasia ossificans progressiva (FOP) ...

    Growth factor signaling pathways are tightly regulated by phosphorylation and include many important kinase targets of interest for drug discovery. Small molecule inhibitors of the bone morphogenetic protein (BMP) receptor kinase ALK2 (ACVR1) are needed urgently to treat the progressively debilitating musculoskeletal disease fibrodysplasia ossificans progressiva (FOP). Dorsomorphin analogues, first identified in zebrafish, remain the only BMP inhibitor chemotype reported to date. By screening an assay panel of 250 recombinant human kinases we identified a highly selective 2-aminopyridine-based inhibitor K02288 with in vitro activity against ALK2 at low nanomolar concentrations similar to the current lead compound LDN-193189. K02288 specifically inhibited the BMP-induced Smad pathway without affecting TGF-β signaling and induced dorsalization of zebrafish embryos. Comparison of the crystal structures of ALK2 with K02288 and LDN-193189 revealed additional contacts in the K02288 complex affording improved shape complementarity and identified the exposed phenol group for further optimization of pharmacokinetics. The discovery of a new chemical series provides an independent pharmacological tool to investigate BMP signaling and offers multiple opportunities for pre-clinical development.


    Organizational Affiliation

    Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Activin receptor type-1A, B, C, D301Homo sapiensMutation(s): 1 
Gene Names: ACVR1ACVRLK2
EC: 2.7.11.30
Find proteins for Q04771 (Homo sapiens)
Explore Q04771 
Go to UniProtKB:  Q04771
NIH Common Fund Data Resources
PHAROS:  Q04771
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LDN
Query on LDN

Download Ideal Coordinates CCD File 
AA [auth D], E [auth A], M [auth B], T [auth C]4-[6-(4-piperazin-1-ylphenyl)pyrazolo[1,5-a]pyrimidin-3-yl]quinoline
C25 H22 N6
CDOVNWNANFFLFJ-UHFFFAOYSA-N
 Ligand Interaction
FLC
Query on FLC

Download Ideal Coordinates CCD File 
FA [auth D] , GA [auth D] , HA [auth D] , K [auth A] , L [auth A] , P [auth B] , Q [auth B] , R [auth B] , 
FA [auth D],  GA [auth D],  HA [auth D],  K [auth A],  L [auth A],  P [auth B],  Q [auth B],  R [auth B],  S [auth B],  X [auth C],  Y [auth C],  Z [auth C]
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth D] , CA [auth D] , DA [auth D] , EA [auth D] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , 
BA [auth D],  CA [auth D],  DA [auth D],  EA [auth D],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  N [auth B],  O [auth B],  U [auth C],  V [auth C],  W [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LDNIC50:  41   nM  BindingDB
LDNIC50:  3.299999952316284   nM  BindingDB
LDNIC50:  17   nM  BindingDB
LDNEC50:  14   nM  BindingDB
LDNIC50:  40.70000076293945   nM  BindingDB
LDNIC50:  0.6700000166893005   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.6α = 90
b = 98.7β = 117.42
c = 83.85γ = 90
Software Package:
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-06-18
    Changes: Database references