4D1X

CDK2 in complex with Luciferin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.194 

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:  

  • 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 ...

    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. Electronic address: richard.engh@uit.no.,The Norwegian Structural Biology Centre, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway.,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.,Lytix Biopharma AS, P.O. Box 6447, Tromsø Science Park, N-9294 Tromsø, Norway.,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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYCLIN-DEPENDENT KINASE 2
A
298Homo sapiensMutation(s): 0 
Gene Names: CDK2 (CDKN2)
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Go to Gene View: CDK2
Go to UniProtKB:  P24941
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ESJ
Query on ESJ

Download SDF File 
Download CCD File 
A
(4S)-2-(6-hydroxy-1,3-benzothiazol-2-yl)-4,5-dihydro-1,3-thiazole-4-carboxylic acid
D-LUCIFERIN
C11 H8 N2 O3 S2
BJGNCJDXODQBOB-SSDOTTSWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.310α = 90.00
b = 72.120β = 90.00
c = 72.290γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
MOLREPphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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