CLK1 with bound pyridoquinazoline

Experimental Data Snapshot

  • Resolution: 2.29 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


New pyrido[3,4-g]quinazoline derivatives as CLK1 and DYRK1A inhibitors: synthesis, biological evaluation and binding mode analysis.

Tazarki, H.Zeinyeh, W.Esvan, Y.J.Knapp, S.Chatterjee, D.Schroder, M.Joerger, A.C.Khiari, J.Josselin, B.Baratte, B.Bach, S.Ruchaud, S.Anizon, F.Giraud, F.Moreau, P.

(2019) Eur J Med Chem 166: 304-317

  • DOI: https://doi.org/10.1016/j.ejmech.2019.01.052
  • Primary Citation of Related Structures:  
    6Q8K, 6Q8P

  • PubMed Abstract: 

    Cdc2-like kinase 1 (CLK1) and dual specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) are involved in the regulation of alternative pre-mRNA splicing. Dysregulation of this process has been linked to cancer progression and neurodegenerative diseases, making CLK1 and DYRK1A important therapeutic targets. Here we describe the synthesis of new pyrido[3,4-g]quinazoline derivatives and the evaluation of the inhibitory potencies of these compounds toward CDK5, CK1, GSK3, CLK1 and DYRK1A. Introduction of aminoalkylamino groups at the 2-position resulted in several compounds with low nanomolar affinity and selective inhibition of CLK1 and/or DYRK1A. Their evaluation on several immortalized or cancerous cell lines showed varying degree of cell viability reduction. Co-crystal structures of CLK1 with two of the most potent compounds revealed two alternative binding modes of the pyrido[3,4-g]quinazoline scaffold that can be exploited for future inhibitor design.

  • Organizational Affiliation

    Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000, Clermont-Ferrand, France; Carthage University, Laboratory of Organic and Analytical Chemistry (ISEFC), Tunis, Tunisia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity protein kinase CLK1339Homo sapiensMutation(s): 0 
Gene Names: CLK1CLK
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FG9

Download Ideal Coordinates CCD File 
C [auth A]~{N}2-(3-morpholin-4-ylpropyl)pyrido[3,4-g]quinazoline-2,10-diamine
C18 H22 N6 O
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A]1,2-ETHANEDIOL
C2 H6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
FG9 Binding MOAD:  6Q8K IC50: 290 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.29 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.848α = 90
b = 64.3β = 109.98
c = 86.339γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-02-27
    Changes: Data collection, Structure summary