2WU7

Crystal Structure of the Human CLK3 in complex with V25


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.1 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:  
    2VAG, 2WU6, 2WU7

  • 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 the ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DUAL SPECIFICITY PROTEIN KINASE CLK3 A381Homo sapiensMutation(s): 0 
Gene Names: CLK3
EC: 2.7.12.1
Find proteins for P49761 (Homo sapiens)
Explore P49761 
Go to UniProtKB:  P49761
NIH Common Fund Data Resources
PHAROS:  P49761
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
V25IC50 :  530   nM  PDBBind
V25IC50:  530   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.87α = 90
b = 62.2β = 97.97
c = 75.37γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
SADABSdata reduction
SAINTdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-12-07
    Changes: Atomic model, Database references, Derived calculations, Other, Refinement description, Structure summary, Version format compliance