6FT8 | pdb_00006ft8

Crystal structure of CLK1 in complex with inhibitor 8g

• PDB DOI: https://doi.org/10.2210/pdb6FT8/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-02-20 Released: 2018-05-16 
• Deposition Author(s): Chaikuad, A., Walter, A., von Delft, F., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Kunick, C., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.195 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

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

• PubMed: 29723265 
• DOI: https://doi.org/10.1371/journal.pone.0196761
• Primary Citation 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.

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Organizational Affiliation: 
• Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Braunschweig, Germany.
Center of Pharmaceutical Engeneering (PVZ), Technische Universität Braunschweig, Braunschweig, Germany.
Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom.
Institute for Pharmaceutical Chemistry, Structural Genomics Consortium and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
ManRos Therapeutics, Hôtel de Recherche, Centre de Perharidy, Roscoff, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 40.27 kDa 
• Atom Count: 3,338 
• Modeled Residue Count: 338 
• Deposited Residue Count: 339 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein kinase CLK1	A	339	Homo sapiens	Mutation(s): 1  Gene Names: CLK1, CLK 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E6T	B [auth A]	3-(3-hydroxyphenyl)-1~{H}-pyrrolo[3,4-g]indol-8-one C16 H10 N2 O2 NIESWLNGCVKLAW-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.195 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.64	α = 90
b = 64.21	β = 127.67
c = 88.36	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-16 
Deposition Author(s): Chaikuad, A., Walter, A., von Delft, F., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Kunick, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

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