6SZM

Crystal structure of the ACVR1 (ALK2) kinase in complex with the compound M4K2009


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Leveraging an Open Science Drug Discovery Model to Develop CNS-Penetrant ALK2 Inhibitors for the Treatment of Diffuse Intrinsic Pontine Glioma.

Smil, D.Wong, J.F.Williams, E.P.Adamson, R.J.Howarth, A.McLeod, D.A.Mamai, A.Kim, S.Wilson, B.J.Kiyota, T.Aman, A.Owen, J.Poda, G.Horiuchi, K.Y.Kuznetsova, E.Ma, H.Hamblin, J.N.Cramp, S.Roberts, O.G.Edwards, A.M.Uehling, D.Al-Awar, R.Bullock, A.N.O'Meara, J.A.Isaac, M.B.

(2020) J Med Chem 63: 10061-10085

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01199
  • Primary Citation of Related Structures:  
    6SZM

  • PubMed Abstract: 

    There are currently no effective chemotherapeutic drugs approved for the treatment of diffuse intrinsic pontine glioma (DIPG), an aggressive pediatric cancer resident in the pons region of the brainstem. Radiation therapy is beneficial but not curative, with the condition being uniformly fatal. Analysis of the genomic landscape surrounding DIPG has revealed that activin receptor-like kinase-2 (ALK2) constitutes a potential target for therapeutic intervention given its dysregulation in the disease. We adopted an open science approach to develop a series of potent, selective, orally bioavailable, and brain-penetrant ALK2 inhibitors based on the lead compound LDN-214117 . Modest structural changes to the C-3, C-4, and C-5 position substituents of the core pyridine ring afforded compounds M4K2009 , M4K2117 , and M4K2163 , each with a superior potency, selectivity, and/or blood-brain barrier (BBB) penetration profile. Robust in vivo pharmacokinetic (PK) properties and tolerability mark these inhibitors as advanced preclinical compounds suitable for further development and evaluation in orthotopic models of DIPG.


  • Organizational Affiliation

    Drug Discovery Program, Ontario Institute for Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Activin receptor type I
A, B
301Homo sapiensMutation(s): 0 
Gene Names: ACVR1
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M2Z (Subject of Investigation/LOI)
Query on M2Z

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
N [auth B]
1-[4-[4-methyl-5-(3,4,5-trimethoxyphenyl)pyridin-3-yl]phenyl]piperazine
C25 H29 N3 O3
RKBYYWVZFBATHQ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
M [auth A],
O [auth B],
S [auth B],
T [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS
Query on DMS

Download Ideal Coordinates CCD File 
P [auth B]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
L [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth A],
Q [auth B],
R [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NH4
Query on NH4

Download Ideal Coordinates CCD File 
K [auth A]AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.338α = 90
b = 84.432β = 131.162
c = 88.136γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2020-10-28
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description