2VAG

Crystal structure of di-phosphorylated human CLK1 in complex with a novel substituted indole inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Specific Clk Inhibitors from a Novel Chemotype for Regulation of Alternative Splicing.

Fedorov, O.Huber, K.Eisenreich, A.Filippakopoulos, P.King, O.Bullock, A.N.Szklarczyk, D.Jensen, L.J.Fabbro, D.Trappe, J.Rauch, U.Bracher, F.Knapp, S.

(2011) Chem.Biol 18: 67

  • DOI: 10.1016/j.chembiol.2010.11.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • There is a growing recognition of the importance of protein kinases in the control of alternative splicing. To define the underlying regulatory mechanisms, highly selective inhibitors are needed. Here, we report the discovery and characterization of ...

    There is a growing recognition of the importance of protein kinases in the control of alternative splicing. To define the underlying regulatory mechanisms, highly selective inhibitors are needed. Here, we report the discovery and characterization of the dichloroindolyl enaminonitrile KH-CB19, a potent and highly specific inhibitor of the CDC2-like kinase isoforms 1 and 4 (CLK1/CLK4). Cocrystal structures of KH-CB19 with CLK1 and CLK3 revealed a non-ATP mimetic binding mode, conformational changes in helix αC and the phosphate binding loop and halogen bonding to the kinase hinge region. KH-CB19 effectively suppressed phosphorylation of SR (serine/arginine) proteins in cells, consistent with its expected mechanism of action. Chemical inhibition of CLK1/CLK4 generated a unique pattern of splicing factor dephosphorylation and had at low nM concentration a profound effect on splicing of the two tissue factor isoforms flTF (full-length TF) and asHTF (alternatively spliced human TF).


    Organizational Affiliation

    University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Old Road Campus Research Building, Oxford OX37DQ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DUAL SPECIFICITY PROTEIN KINASE CLK1
A
339Homo sapiensMutation(s): 0 
Gene Names: CLK1 (CLK)
EC: 2.7.12.1
Find proteins for P49759 (Homo sapiens)
Go to Gene View: CLK1
Go to UniProtKB:  P49759
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V25
Query on V25

Download SDF File 
Download CCD File 
A
ethyl 3-[(E)-2-amino-1-cyanoethenyl]-6,7-dichloro-1-methyl-1H-indole-2-carboxylate
C15 H13 Cl2 N3 O2
CXJCGSPAPOTTSF-VURMDHGXSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
V25IC50: 19.7 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.950α = 90.00
b = 64.108β = 118.17
c = 78.894γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Refinement description, Version format compliance
  • Version 1.2: 2011-12-07
    Type: Database references, Structure summary