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 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report



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

  • 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 neurodegenerativ ...

    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. Electronic address: pascale.moreau@uca.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dual specificity protein kinase CLK1 ABC339Homo sapiensMutation(s): 0 
Gene Names: CLK1CLK
EC: 2.7.12.1
Find proteins for P49759 (Homo sapiens)
Explore P49759 
Go to UniProtKB:  P49759
NIH Common Fund Data Resources
PHAROS:  P49759
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HQB
Query on HQB

Download Ideal Coordinates CCD File 
A, B, C
~{N}-methyl-10-nitro-pyrido[3,4-g]quinazolin-2-amine
C12 H9 N5 O2
WJQCMHKMNXKJQR-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • 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



Entry History 

Revision History 

  • Version 1.0: 2019-02-20
    Type: Initial release