CDK2 in complex with a Luciferin derivate

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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Ligand Structure Quality Assessment 

This is version 2.1 of the entry. See complete history


Luciferin and Derivatives as a Dyrk Selective Scaffold for the Design of Protein Kinase Inhibitors.

Rothweiler, U.Eriksson, J.Stensen, W.Leeson, F.Engh, R.A.Svendsen, J.S.

(2015) Eur J Med Chem 94: 140

  • DOI: https://doi.org/10.1016/j.ejmech.2015.02.035
  • Primary Citation of Related Structures:  
    4D1X, 4D1Z

  • PubMed Abstract: 

    D-Luciferin is widely used as a substrate in luciferase catalysed bioluminescence assays for in vitro studies. However, little is known about cross reactivity and potential interference of D-luciferin with other enzymes. We serendipitously found that firefly luciferin inhibited the CDK2/Cyclin A protein kinase. Inhibition profiling of D-luciferin over a 103-protein kinase panel showed significant inhibition of a small set of protein kinases, in particular the DYRK-family, but also other members of the CMGC-group, including ERK8 and CK2. Inhibition profiling on a 16-member focused library derived from D-luciferin confirms that D-luciferin represents a DYRK-selective chemotype of fragment-like molecular weight. Thus, observation of its inhibitory activity and the initial SAR information reported here promise to be useful for further design of protein kinase inhibitors with related scaffolds.

  • Organizational Affiliation

    The Norwegian Structural Biology Centre, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYCLIN-DEPENDENT KINASE 2298Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
PHAROS:  P24941
GTEx:  ENSG00000123374 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24941
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on WG8

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
(4S)-2-(8-hydroxyquinolin-2-yl)-4,5-dihydro-1,3-thiazole-4-carboxylic acid
C13 H10 N2 O3 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.83α = 90
b = 72.4β = 90
c = 73.06γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-03-25
    Changes: Database references
  • Version 1.2: 2015-09-02
    Changes: Structure summary
  • Version 2.0: 2019-10-23
    Changes: Atomic model, Data collection, Other
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description