8P04 | pdb_00008p04

Crystal structure of human CLK1 in complex with Leucettinib-92


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.259 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.209 (Depositor) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Leucettinibs, a Class of DYRK/CLK Kinase Inhibitors Inspired by the Marine Sponge Natural Product Leucettamine B.

Deau, E.Lindberg, M.F.Miege, F.Roche, D.George, N.George, P.Kramer, A.Knapp, S.Meijer, L.

(2023) J Med Chem 66: 10694-10714

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00884
  • Primary Citation Related Structures: 
    8P04, 8P05

  • PubMed Abstract: 

    Dual-specificity, tyrosine phosphorylation-regulated kinases (DYRKs) and cdc2-like kinases (CLKs) recently attracted attention due to their central involvement in various pathologies. We here describe a family of DYRK/CLK inhibitors derived from Leucettines and the marine natural product Leucettamine B. Forty-five N 2-functionalized 2-aminoimidazolin-4-ones bearing a fused [6 + 5]-heteroarylmethylene were synthesized. Benzothiazol-6-ylmethylene was selected as the most potent residue among 15 different heteroarylmethylenes. 186 N 2-substituted 2-aminoimidazolin-4-ones bearing a benzothiazol-6-ylmethylene, collectively named Leucettinibs, were synthesized and extensively characterized. Subnanomolar IC 50 (0.5-20 nM on DYRK1A) inhibitors were identified and one Leucettinib was modeled in DYRK1A and co-crystallized with CLK1 and the weaker inhibited off-target CSNK2A1. Kinase-inactive isomers of Leucettinibs (>3-10 μM on DYRK1A), named iso-Leucettinibs, were synthesized and characterized as suitable negative control compounds for functional experiments. Leucettinibs, but not iso-Leucettinibs, inhibit the phosphorylation of DYRK1A substrates in cells. Leucettinibs provide new research tools and potential leads for further optimization toward therapeutic drug candidates.


  • Organizational Affiliation
    • Perha Pharmaceuticals, Perharidy, 29680 Roscoff, France.

Macromolecule Content 

  • Total Structure Weight: 39.96 kDa 
  • Atom Count: 2,539 
  • Modeled Residue Count: 321 
  • Deposited Residue Count: 339 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dual specificity protein kinase CLK1339Homo sapiensMutation(s): 0 
Gene Names: CLK1CLK
EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49759 (Homo sapiens)
Explore P49759 
Go to UniProtKB:  P49759
PHAROS:  P49759
GTEx:  ENSG00000013441 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49759
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WAK
(Subject of Investigation/LOI)

Query on WAK



Download:Ideal Coordinates CCD File
B [auth A](4~{Z})-2-(1-adamantylamino)-4-(1,3-benzothiazol-6-ylmethylidene)-1~{H}-imidazol-5-one
C21 H22 N4 O S
HEVBCYZPXGZFGS-KDBINBPISA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.259 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.209 (Depositor) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.134α = 90
b = 64.026β = 118.49
c = 70.571γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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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: 2023-05-17
    Type: Initial release
  • Version 2.0: 2023-05-24
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references