Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.37 kDa 
• Atom Count: 2388 
• Modelled Residue Count: 281 
• Deposited Residue Count: 298 
• Unique protein chains: 1

1KE7

CYCLIN-DEPENDENT KINASE 2 (CDK2) COMPLEXED WITH 3-{[(2,2-DIOXIDO-1,3-DIHYDRO-2-BENZOTHIEN-5-YL)AMINO]METHYLENE}-5-(1,3-OXAZOL-5-YL)-1,3-DIHYDRO-2H-INDOL-2-ONE

• PDB DOI: 10.2210/pdb1KE7/pdb

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


• Deposited: 2001-11-14 Released: 2002-05-14 
• Deposition Author(s): Bramson, H.N., Corona, J., Davis, S.T., Dickerson, S.H., Edelstein, M., Frye, S.V., Gampe, R.T., Hassell, A.H., Shewchuk, L.M., Kuyper, L.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.235 
• R-Value Work: 0.191 

Literature

Oxindole-based inhibitors of cyclin-dependent kinase 2 (CDK2): design, synthesis, enzymatic activities, and X-ray crystallographic analysis.

Bramson, H.N., Corona, J., Davis, S.T., Dickerson, S.H., Edelstein, M., Frye, S.V., Gampe Jr., R.T., Harris, P.A., Hassell, A., Holmes, W.D., Hunter, R.N., Lackey, K.E., Lovejoy, B., Luzzio, M.J., Montana, V., Rocque, W.J., Rusnak, D., Shewchuk, L., Veal, J.M., Walker, D.H., Kuyper, L.F.

(2001) J Med Chem 44: 4339-4358

• PubMed: 11728181 
• DOI: 10.1021/jm010117d
• Primary Citation of Related Structures:  
  1KE5, 1KE6, 1KE7, 1KE8, 1KE9


• PubMed Abstract: 
  

Two closely related classes of oxindole-based compounds, 1H-indole-2,3-dione 3-phenylhydrazones and 3-(anilinomethylene)-1,3-dihydro-2H-indol-2-ones, were shown to potently inhibit cyclin-dependent kinase 2 (CDK2). The initial lead compound was prepared as a homologue of the 3-benzylidene-1,3-dihydro-2H-indol-2-one class of kinase inhibitor. Crystallographic analysis of the lead compound bound to CDK2 provided the basis for analogue design. A semiautomated method of ligand docking was used to select compounds for synthesis, and a number of compounds with low nanomolar inhibitory activity versus CDK2 were identified. Enzyme binding determinants for several analogues were evaluated by X-ray crystallography. Compounds in this series inhibited CDK2 with a potency approximately 10-fold greater than that for CDK1. Members of this class of inhibitor cause an arrest of the cell cycle and have shown potential utility in the prevention of chemotherapy-induced alopecia.

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Organizational Affiliation: 

GlaxoSmithKline Inc., Five Moore Drive, Research Triangle Park, North Carolina 27709, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein kinase 2	A	298	Homo sapiens	Mutation(s): 0  Gene Names: CDK2, CDKN2 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens) Explore P24941  Go to UniProtKB:  P24941
PHAROS:  P24941

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LS3	B [auth A]	3-{[(2,2-DIOXIDO-1,3-DIHYDRO-2-BENZOTHIEN-5-YL)AMINO]METHYLENE}-5-(1,3-OXAZOL-5-YL)-1,3-DIHYDRO-2H-INDOL-2-ONE C20 H15 N3 O4 S FTQYGMLRLRXBPT-IDUWFGFVSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
LS3	BindingDB:  1KE7	IC50: 8.9 (nM) from 1 assay(s)
	Binding MOAD:  1KE7	IC50: 8.9 (nM) from 1 assay(s)
	PDBBind:  1KE7	IC50: 8.9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.235 
• R-Value Work: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.76	α = 90
b = 73.78	β = 90
c = 54	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-11-14 
• Released Date: 2002-05-14 
Deposition Author(s): Bramson, H.N., Corona, J., Davis, S.T., Dickerson, S.H., Edelstein, M., Frye, S.V., Gampe, R.T., Hassell, A.H., Shewchuk, L.M., Kuyper, L.F.

Revision History  

• Version 1.0: 2002-05-14
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-31
  Changes: Experimental preparation