6FT7 | pdb_00006ft7

Crystal structure of CLK3 in complex with compound 8a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 
    0.235 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.1 of the entry. See complete history


Literature

Molecular structures of cdc2-like kinases in complex with a new inhibitor chemotype.

Walter, A.Chaikuad, A.Helmer, R.Loaec, N.Preu, L.Ott, I.Knapp, S.Meijer, L.Kunick, C.

(2018) PLoS One 13: e0196761-e0196761

  • DOI: https://doi.org/10.1371/journal.pone.0196761
  • Primary Citation of Related Structures:  
    6FT7, 6FT8, 6FT9

  • PubMed Abstract: 

    Cdc2-like kinases (CLKs) represent a family of serine-threonine kinases involved in the regulation of splicing by phosphorylation of SR-proteins and other splicing factors. Although compounds acting against CLKs have been described, only a few show selectivity against dual-specificity tyrosine phosphorylation regulated-kinases (DYRKs). We here report a novel CLK inhibitor family based on a 6,7-dihydropyrrolo[3,4-g]indol-8(1H)-one core scaffold. Within the series, 3-(3-chlorophenyl)-6,7-dihydropyrrolo[3,4-g]indol-8(1H)-one (KuWal151) was identified as inhibitor of CLK1, CLK2 and CLK4 with a high selectivity margin towards DYRK kinases. The compound displayed a potent antiproliferative activity in an array of cultured cancer cell lines. The X-ray structure analyses of three members of the new compound class co-crystallized with CLK proteins corroborated a molecular binding mode predicted by docking studies.


  • Organizational Affiliation

    Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Braunschweig, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity protein kinase CLK3
A, B
360Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E6Q
Query on E6Q

Download Ideal Coordinates CCD File 
DA [auth B],
M [auth A]
3-phenyl-1~{H}-pyrrolo[3,4-g]indol-8-one
C16 H10 N2 O
YJGNZVVUIPDSRL-UHFFFAOYSA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
J [auth A]
K [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.76α = 90
b = 116.83β = 92.75
c = 69.91γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata 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 E6QClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description