9EZ3 | pdb_00009ez3

Crystal structure of human CLK3 bound to RN129


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.268 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Type II kinase inhibitors that target Parkinson's disease-associated LRRK2.

Raig, N.D.Surridge, K.J.Sanz-Murillo, M.Dederer, V.Kramer, A.Schwalm, M.P.Lattal, N.M.Elson, L.Chatterjee, D.Mathea, S.Hanke, T.Leschziner, A.E.Reck-Peterson, S.L.Knapp, S.

(2025) Sci Adv 11: eadt2050-eadt2050

  • DOI: https://doi.org/10.1126/sciadv.adt2050
  • Primary Citation of Related Structures:  
    9DMI, 9EZ3

  • PubMed Abstract: 

    Increased kinase activity of leucine-rich repeat kinase 2 (LRRK2) is associated with Parkinson's disease (PD). Numerous LRRK2-selective type I kinase inhibitors have been developed, and some have entered clinical trials. Here, to our knowledge, we present the first type II kinase inhibitors that target LRRK2. Targeting the inactive conformation of LRRK2 is functionally distinct from targeting the active-like conformation using type I inhibitors. We designed these inhibitors with a combinatorial chemistry approach fusing selective LRRK2 type I and promiscuous type II inhibitors using iterative cycles of synthesis supported by structural biology and activity testing. Our lead compounds are selective and potent toward both LRRK2 and LRRK1, a close relative of LRRK2. Through cellular assays, cryo-electron microscopy structural analysis, and in vitro motility assays, we show that our inhibitors stabilize the open, inactive LRRK2 kinase conformation. These new conformation-specific compounds will be invaluable as tools to study LRRK2's function and regulation and expand the potential therapeutic options for PD.


  • Organizational Affiliation
    • Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity protein kinase CLK3360Homo sapiensMutation(s): 0 
Gene Names: CLK3
EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49761 (Homo sapiens)
Explore P49761 
Go to UniProtKB:  P49761
PHAROS:  P49761
GTEx:  ENSG00000179335 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49761
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.268 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.587α = 90
b = 74.587β = 90
c = 97.035γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Innovative Medicines InitiativeSwitzerland875510

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Database references, Structure summary