Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34256.81 
• Atom Count: 2180 
• Residue Count: 298 
• Unique protein chains: 1

4D1X

CDK2 in complex with Luciferin

• DOI: 10.2210/pdb4D1X/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2014-05-05 Released: 2015-03-18 
• Deposition Author(s): Rothweiler, U., Engh, R.A.

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Experimental Data Snapshot

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

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

• PubMed: 25768698 
• DOI: 10.1016/j.ejmech.2015.02.035
• Primary Citation of Related Structures:  
  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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CYCLIN-DEPENDENT KINASE 2	A	298	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ESJ	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

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 = 53.310	α = 90.00
b = 72.120	β = 90.00
c = 72.290	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data scaling
MOLREP	phasing
XDS	data reduction
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-05 
• Released Date: 2015-03-18 
• Deposition Author(s): Rothweiler, U., Engh, R.A.

Revision History 

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