4D1X

CDK2 in complex with Luciferin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

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

  • 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 fir ...

    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: 

    Lytix Biopharma AS, P.O. Box 6447, Tromsø Science Park, N-9294 Tromsø, Norway; Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway. Electronic address: john-sigurd.svendsen@uit.no.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLIN-DEPENDENT KINASE 2 A298Homo sapiensMutation(s): 0 
Gene Names: CDK2, CDKN2
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS:  P24941
GTEx:  ENSG00000123374
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ESJ
Query on ESJ
Download Ideal Coordinates CCD File 
A
(4S)-2-(6-hydroxy-1,3-benzothiazol-2-yl)-4,5-dihydro-1,3-thiazole-4-carboxylic acid
C11 H8 N2 O3 S2
BJGNCJDXODQBOB-SSDOTTSWSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.31α = 90
b = 72.12β = 90
c = 72.29γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-03-25
    Changes: Database references