9CE4

Structure of CHK1 10-pt. mutant complex with LRRK2 indazole inhibitor compound 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery and Optimization of N-Heteroaryl Indazole LRRK2 Inhibitors.

Logan, K.M.Kaplan, W.Simov, V.Zhou, H.Li, D.Torres, L.Morriello, G.J.Acton, J.J.Pio, B.Chen, Y.H.Keylor, M.H.Johnson, R.Kattar, S.D.Chau, R.Yan, X.Ardolino, M.Zarate, C.Otte, K.M.Palte, R.L.Xiong, T.McMinn, S.E.Lin, S.Neelamkavil, S.F.Liu, P.Su, J.Hegde, L.G.Woodhouse, J.D.Moy, L.Y.Ciaccio, P.J.Piesvaux, J.Zebisch, M.Henry, C.Barker, J.Wood, H.B.Kennedy, M.E.DiMauro, E.F.Fell, M.J.Fuller, P.H.

(2024) J Med Chem 67: 16807-16819

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01627
  • Primary Citation of Related Structures:  
    9CE4

  • PubMed Abstract: 

    Inhibition of leucine-rich repeat kinase 2 is a genetically supported mechanism for the treatment of Parkinson's disease. We previously disclosed the discovery of an indazole series lead that demonstrated both safety and translational risks. The safety risks were hypothesized to be of unknown origin, so structural diversity in subsequent chemical matter was prioritized. The translational risks were identified due to a low brain Kp u,u in nonhuman primate studies, which raised concern over the use of an established peripheral biomarker as a surrogate for central target engagement. Given these challenges, the team sought to leverage structure- and property-based drug design and expanded efflux transporter profiling to identify structurally distinct leads with enhanced CNS drug-likeness. Herein, we describe the discovery of a "reinvented" indazole series with improved physicochemical properties and efflux transporter profiles while maintaining excellent potency and off-target kinase selectivity, which resulted in advanced lead, compound 23 .


  • Organizational Affiliation

    Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase Chk1268Homo sapiensMutation(s): 10 
Gene Names: CHEK1CHK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14757 (Homo sapiens)
Explore O14757 
Go to UniProtKB:  O14757
PHAROS:  O14757
GTEx:  ENSG00000149554 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14757
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AV4 (Subject of Investigation/LOI)
Query on A1AV4

Download Ideal Coordinates CCD File 
B [auth A](1S,4r)-4-[(1P)-5-chloro-1-(1-methyl-1H-pyrazol-4-yl)-1H-indazol-6-yl]-1-(oxetan-3-yl)piperidin-1-ium
C19 H23 Cl N5 O
QNTMOHJVKJNXDF-UHFFFAOYSA-O
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.896α = 90
b = 65.238β = 101.49
c = 53.785γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
autoPROCdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release
  • Version 1.1: 2024-10-02
    Changes: Database references