5U6I

Discovery of MLi-2, an Orally Available and Selective LRRK2 Inhibitor that Reduces Brain Kinase Activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of a 3-(4-Pyrimidinyl) Indazole (MLi-2), an Orally Available and Selective Leucine-Rich Repeat Kinase 2 (LRRK2) Inhibitor that Reduces Brain Kinase Activity.

Scott, J.D.DeMong, D.E.Greshock, T.J.Basu, K.Dai, X.Harris, J.Hruza, A.Li, S.W.Lin, S.I.Liu, H.Macala, M.K.Hu, Z.Mei, H.Zhang, H.Walsh, P.Poirier, M.Shi, Z.C.Xiao, L.Agnihotri, G.Baptista, M.A.Columbus, J.Fell, M.J.Hyde, L.A.Kuvelkar, R.Lin, Y.Mirescu, C.Morrow, J.A.Yin, Z.Zhang, X.Zhou, X.Chang, R.K.Embrey, M.W.Sanders, J.M.Tiscia, H.E.Drolet, R.E.Kern, J.T.Sur, S.M.Renger, J.J.Bilodeau, M.T.Kennedy, M.E.Parker, E.M.Stamford, A.W.Nargund, R.McCauley, J.A.Miller, M.W.

(2017) J Med Chem 60: 2983-2992

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00045
  • Primary Citation of Related Structures:  
    5U6I

  • PubMed Abstract: 

    Leucine-rich repeat kinase 2 (LRRK2) is a large, multidomain protein which contains a kinase domain and GTPase domain among other regions. Individuals possessing gain of function mutations in the kinase domain such as the most prevalent G2019S mutation have been associated with an increased risk for the development of Parkinson's disease (PD). Given this genetic validation for inhibition of LRRK2 kinase activity as a potential means of affecting disease progression, our team set out to develop LRRK2 inhibitors to test this hypothesis. A high throughput screen of our compound collection afforded a number of promising indazole leads which were truncated in order to identify a minimum pharmacophore. Further optimization of these indazoles led to the development of MLi-2 (1): a potent, highly selective, orally available, brain-penetrant inhibitor of LRRK2.


  • Organizational Affiliation

    Merck & Co., Inc. , 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1366Rattus norvegicusMutation(s): 0 
Gene Names: Mapk1Erk2MapkPrkm1
EC: 2.7.11.24
UniProt
Find proteins for P63086 (Rattus norvegicus)
Explore P63086 
Go to UniProtKB:  P63086
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63086
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.178α = 90
b = 91.416β = 90
c = 62.541γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
autoPROCdata scaling
BUSTERrefinement
MOLREPphasing
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-04-26
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description