2DUV

Structure of CDK2 with a 3-hydroxychromones

• PDB DOI: https://doi.org/10.2210/pdb2DUV/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• 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: 2.20 Å
• R-Value Free: 0.310 
• R-Value Work: 0.264 
• R-Value Observed: 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: https://doi.org/10.1016/j.bmcl.2006.12.011
• Primary Citation of Related Structures:  
  2DUV


• 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]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.38 kDa 
• Atom Count: 2,301 
• Modelled Residue Count: 272 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein kinase 2	A	298	Homo sapiens	Mutation(s): 0  EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens) Explore P24941  Go to UniProtKB:  P24941
PHAROS:  P24941 GTEx:  ENSG00000123374

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
371	B [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
371	BindingDB:  2DUV	IC50: 87 (nM) from 1 assay(s)
	PDBBind:  2DUV	IC50: 87 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.310 
• R-Value Work: 0.264 
• R-Value Observed: 0.264 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.629	α = 90
b = 71.389	β = 90
c = 72.061	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations