2VAG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6TW2


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:  
    2WU6, 2WU7, 2VAG

  • 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 dichloroindolyl enaminonitrile KH-CB19, a potent and highly specific inhibitor of the CDC2-like kinase isoforms 1 and 4 (CLK1/CLK4) ...

    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 CLK1 A339Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V25
Query on V25

Download Ideal Coordinates 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
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
AL-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
V25IC50:  19.700000762939453   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.95α = 90
b = 64.108β = 118.17
c = 78.894γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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