6Q8P

Structure of CLK1 with bound N-methyl-10-nitropyrido[3,4-g]quinazolin-2-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.244 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity protein kinase CLK1
A, B, C
339Homo 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.244 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.791α = 90
b = 117.553β = 99
c = 91.911γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HQBClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description