Crystal Structure of the Human CLK3 in complex with V25

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

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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: https://doi.org/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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DUAL SPECIFICITY PROTEIN KINASE CLK3381Homo sapiensMutation(s): 0 
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
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on V25

Download Ideal Coordinates CCD File 
B [auth A]ethyl 3-[(E)-2-amino-1-cyanoethenyl]-6,7-dichloro-1-methyl-1H-indole-2-carboxylate
C15 H13 Cl2 N3 O2
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
O4 S
Query on CL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
Binding Affinity Annotations 
IDSourceBinding Affinity
V25 Binding MOAD:  2WU7 IC50: 530 (nM) from 1 assay(s)
PDBBind:  2WU7 IC50: 530 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • 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
SADABSdata reduction
SAINTdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • 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