6I3U

Optimization of potent and selective ATM inhibitors suitable for a proof-of-concept study in Huntington's disease models


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Optimization of Potent and Selective Ataxia Telangiectasia-Mutated Inhibitors Suitable for a Proof-of-Concept Study in Huntington's Disease Models.

Toledo-Sherman, L.Breccia, P.Cachope, R.Bate, J.R.Angulo-Herrera, I.Wishart, G.Matthews, K.L.Martin, S.L.Cox, H.C.McAllister, G.Penrose, S.D.Vater, H.Esmieu, W.Van de Poel, A.Van de Bospoort, R.Strijbosch, A.Lamers, M.Leonard, P.Jarvis, R.E.Blackaby, W.Barnes, K.Eznarriaga, M.Dowler, S.Smith, G.D.Fischer, D.F.Lazari, O.Yates, D.Rose, M.Jang, S.W.Munoz-Sanjuan, I.Dominguez, C.

(2019) J Med Chem 62: 2988-3008

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01819
  • Primary Citation of Related Structures:  
    6I3U

  • PubMed Abstract: 

    Genetic and pharmacological evidence indicates that the reduction of ataxia telangiectasia-mutated (ATM) kinase activity can ameliorate mutant huntingtin (mHTT) toxicity in cellular and animal models of Huntington's disease (HD), suggesting that selective inhibition of ATM could provide a novel clinical intervention to treat HD. Here, we describe the development and characterization of ATM inhibitor molecules to enable in vivo proof-of-concept studies in HD animal models. Starting from previously reported ATM inhibitors, we aimed with few modifications to increase brain exposure by decreasing P-glycoprotein liability while maintaining potency and selectivity. Here, we report brain-penetrant ATM inhibitors that have robust pharmacodynamic (PD) effects consistent with ATM kinase inhibition in the mouse brain and an understandable pharmacokinetic/PD (PK/PD) relationship. Compound 17 engages ATM kinase and shows robust dose-dependent inhibition of X-ray irradiation-induced KAP1 phosphorylation in the mouse brain. Furthermore, compound 17 protects against mHTT (Q73)-induced cytotoxicity in a cortical-striatal cell model of HD.


  • Organizational Affiliation

    CHDI Management/CHDI Foundation , 6080 Center Drive , Los Angeles , California 90045 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase catalytic subunit type 3615Homo sapiensMutation(s): 5 
Gene Names: PIK3C3VPS34
EC: 2.7.1.137
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NEB9 (Homo sapiens)
Explore Q8NEB9 
Go to UniProtKB:  Q8NEB9
PHAROS:  Q8NEB9
GTEx:  ENSG00000078142 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NEB9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H2E
Query on H2E

Download Ideal Coordinates CCD File 
B [auth A]2-morpholin-4-yl-6-[7-[(2~{R})-1-morpholin-4-ylpropan-2-yl]oxy-9~{H}-thioxanthen-4-yl]pyran-4-one
C29 H32 N2 O5 S
HRZBUHAVTBTHTM-HXUWFJFHSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
H2E Binding MOAD:  6I3U IC50: 0.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.17α = 90
b = 167.17β = 90
c = 61.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-03-27
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-10
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description