8E80

Structure of LRRK2-CHK1 10-pt. mutant complex with heteroaryl-1H-indazole LRRK2 inhibitor 14


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery and Optimization of Potent, Selective, and Brain-Penetrant 1-Heteroaryl-1 H -Indazole LRRK2 Kinase Inhibitors for the Treatment of Parkinson's Disease.

Candito, D.A.Simov, V.Gulati, A.Kattar, S.Chau, R.W.Lapointe, B.T.Methot, J.L.DeMong, D.E.Graham, T.H.Kurukulasuriya, R.Keylor, M.H.Tong, L.Morriello, G.J.Acton, J.J.Pio, B.Liu, W.Scott, J.D.Ardolino, M.J.Martinot, T.A.Maddess, M.L.Yan, X.Gunaydin, H.Palte, R.L.McMinn, S.E.Nogle, L.Yu, H.Minnihan, E.C.Lesburg, C.A.Liu, P.Su, J.Hegde, L.G.Moy, L.Y.Woodhouse, J.D.Faltus, R.Xiong, T.Ciaccio, P.Piesvaux, J.A.Otte, K.M.Kennedy, M.E.Bennett, D.J.DiMauro, E.F.Fell, M.J.Neelamkavil, S.Wood, H.B.Fuller, P.H.Ellis, J.M.

(2022) J Med Chem 65: 16801-16817

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01605
  • Primary Citation of Related Structures:  
    8E80, 8E81

  • PubMed Abstract: 

    Inhibition of leucine-rich repeat kinase 2 (LRRK2) kinase activity represents a genetically supported, chemically tractable, and potentially disease-modifying mechanism to treat Parkinson's disease. Herein, we describe the optimization of a novel series of potent, selective, central nervous system (CNS)-penetrant 1-heteroaryl-1 H -indazole type I (ATP competitive) LRRK2 inhibitors. Type I ATP-competitive kinase physicochemical properties were integrated with CNS drug-like properties through a combination of structure-based drug design and parallel medicinal chemistry enabled by sp 3 -sp 2 cross-coupling technologies. This resulted in the discovery of a unique sp 3 -rich spirocarbonitrile motif that imparted extraordinary potency, pharmacokinetics, and favorable CNS drug-like properties. The lead compound, 25 , demonstrated exceptional on-target potency in human peripheral blood mononuclear cells, excellent off-target kinase selectivity, and good brain exposure in rat, culminating in a low projected human dose and a pre-clinical safety profile that warranted advancement toward pre-clinical candidate enabling studies.


  • Organizational Affiliation

    Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase Chk1297Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UUF (Subject of Investigation/LOI)
Query on UUF

Download Ideal Coordinates CCD File 
B [auth A]2-[(1r,4r)-2-{(6P)-6-[(6M)-6-(1H-pyrazol-5-yl)-1H-indazol-1-yl]pyrimidin-4-yl}-2-azabicyclo[2.1.1]hexan-4-yl]propan-2-ol
C22 H23 N7 O
VGHHZMPDXMQZDE-CIEDQVTBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.04α = 90
b = 65.93β = 100.18
c = 55.14γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2023-02-22 
  • Deposition Author(s): Palte, R.L.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description