1KE8 | pdb_00001ke8

CYCLIN-DEPENDENT KINASE 2 (CDK2) COMPLEXED WITH 4-{[(2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]AMINO}-N-(1,3-THIAZOL-2-YL)BENZENESULFONAMIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.228 (Depositor) 
  • R-Value Work: 
    0.187 (Depositor), 0.199 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

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

  • DOI: https://doi.org/10.1021/jm010117d
  • Primary Citation 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.


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

Macromolecule Content 

  • Total Structure Weight: 34.37 kDa 
  • Atom Count: 2,406 
  • Modeled Residue Count: 282 
  • Deposited Residue Count: 298 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CELL DIVISION PROTEIN KINASE 2298Homo sapiensMutation(s): 0 
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
GTEx:  ENSG00000123374 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24941
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LS4

Query on LS4



Download:Ideal Coordinates CCD File
B [auth A]4-{[(2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]AMINO}-N-(1,3-THIAZOL-2-YL)BENZENESULFONAMIDE
C18 H14 N4 O3 S2
BOMPRXSVSIPRDT-PTNGSMBKSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.228 (Depositor) 
  • R-Value Work:  0.187 (Depositor), 0.199 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.53α = 90
b = 74.04β = 90
c = 54.08γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description