Crystal structure of CLK2 in complex with CX-4945

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.203 

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Structural Basis for the Selective Inhibition of Cdc2-Like Kinases by CX-4945.

Lee, J.Y.Yun, J.S.Kim, W.K.Chun, H.S.Jin, H.Cho, S.Chang, J.H.

(2019) Biomed Res Int 2019: 6125068-6125068

  • DOI: https://doi.org/10.1155/2019/6125068
  • Primary Citation of Related Structures:  
    6KHD, 6KHE, 6KHF

  • PubMed Abstract: 

    Cdc2-like kinases (CLKs) play a crucial role in the alternative splicing of eukaryotic pre-mRNAs through the phosphorylation of serine/arginine-rich proteins (SR proteins). Dysregulation of this processes is linked with various diseases including cancers, neurodegenerative diseases, and many genetic diseases. Thus, CLKs have been regarded to have a potential as a therapeutic target and significant efforts have been exerted to discover an effective inhibitor. In particular, the small molecule CX-4945, originally identified as an inhibitor of casein kinase 2 (CK2), was further revealed to have a strong CLK-inhibitory activity. Four isoforms of CLKs (CLK1, CLK2, CLK3, and CLK4) can be inhibited by CX-4945, with the highest inhibitory effect on CLK2. This study aimed to elucidate the structural basis of the selective inhibitory effect of CX-4945 on different isoforms of CLKs. We determined the crystal structures of CLK1, CLK2, and CLK3 in complex with CX-4945 at resolutions of 2.4 Å, 2.8 Å, and 2.6 Å, respectively. Comparative analysis revealed that CX-4945 was bound in the same active site pocket of the CLKs with similar interacting networks. Intriguingly, the active sites of CLK/CX-4945 complex structures had different sizes and electrostatic surface charge distributions. The active site of CLK1 was somewhat narrow and contained a negatively charged patch. CLK3 had a protruded Lys248 residue in the entrance of the active site pocket. In addition, Ala319, equivalent to Val324 (CLK1) and Val326 (CLK2), contributed to the weak hydrophobic interactions with the benzonaphthyridine ring of CX-4945. In contrast, the charge distribution pattern of CLK2 was the weakest, favoring its interactions with benzonaphthyridine ring. Thus, the relatively strong binding affinities of CX-4945 with CLK2 are consistent with its strong inhibitory effect defined in the previous study. These results may provide insights into structure-based drug discovery processes.

  • Organizational Affiliation

    Department of Biology Education, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity protein kinase CLK2499Homo sapiensMutation(s): 0 
Gene Names: CLK2
UniProt & NIH Common Fund Data Resources
Find proteins for P49760 (Homo sapiens)
Explore P49760 
Go to UniProtKB:  P49760
PHAROS:  P49760
GTEx:  ENSG00000176444 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49760
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3NG (Subject of Investigation/LOI)
Query on 3NG

Download Ideal Coordinates CCD File 
B [auth A]5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid
C19 H12 Cl N3 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
3NG BindingDB:  6KHE IC50: min: 3.8, max: 4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.203 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.627α = 90
b = 75.627β = 90
c = 161.825γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references