Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34379.89 
• Atom Count: 2227 
• Residue Count: 298 
• Unique protein chains: 1

2DUV

Structure of CDK2 with a 3-hydroxychromones

• DOI: 10.2210/pdb2DUV/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• Deposited: 2006-07-27 Released: 2007-01-27 
• Deposition Author(s): Kim, K.H., Lee, J., Park, T., Jeong, S., Hong, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.310 
• R-Value Work: 0.264 

Literature

3-Hydroxychromones as cyclin-dependent kinase inhibitors: synthesis and biological evaluation.

Lee, J., Park, T., Jeong, S., Kim, K.H., Hong, C.

(2007) Bioorg.Med.Chem.Lett. 17: 1284-1287

• PubMed: 17178224 
• DOI: 10.1016/j.bmcl.2006.12.011


• PubMed Abstract: 
  

A novel series of 3-hydroxychromones were prepared and found to be CDK inhibitors. Isothiazolidine 1,1-dioxide analogues showed potent CDK1 and CDK2 inhibitory activities and inhibited proliferation of EJ, HCT116, SW620, and MDAMB468 cancer cells.

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Organizational Affiliation: 

Department of Chemistry, Keimyung University, 1000 Sindang-Dong, Dalseo-Gu, Daegu 704-701, South Korea. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cell division protein 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
371	A	2-(3,4-DIHYDROXYPHENYL)-8-(1,1-DIOXIDOISOTHIAZOLIDIN-2-YL)-3-HYDROXY-6-METHYL-4H-CHROMEN-4-ONE C19 H17 N O7 S CEXBEGBNDJVZPK-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
371	IC50: 87 nM (100) BINDINGDB
371	IC50: 87 nM BINDINGMOAD
371	IC50: 87 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.310 
• R-Value Work: 0.264 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 53.629	α = 90.00
b = 71.389	β = 90.00
c = 72.061	γ = 90.00

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-07-27 
• Released Date: 2007-01-27 
• Deposition Author(s): Kim, K.H., Lee, J., Park, T., Jeong, S., Hong, C.

Revision History 

• Version 1.0: 2007-01-27
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance