1R78

CDK2 complex with a 4-alkynyl oxindole inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A new series of potent oxindole inhibitors of CDK2

Luk, K.-C.Simcox, M.E.Schutt, A.Rowan, K.Thompson, T.Chen, Y.Kammlott, U.DePinto, W.Dunten, P.Dermatakis, A.

(2004) Bioorg.Med.Chem.Lett. 14: 913-917

  • DOI: 10.1016/j.bmcl.2003.12.009

  • PubMed Abstract: 
  • A novel series of oxindole-type inhibitors of CDK2 that have heteroatom substituted alkynyl moieties at their C-4 position is described. These novel 4-alkynyl-substituted inhibitors have superior potency relative to their parent compound in free enzy ...

    A novel series of oxindole-type inhibitors of CDK2 that have heteroatom substituted alkynyl moieties at their C-4 position is described. These novel 4-alkynyl-substituted inhibitors have superior potency relative to their parent compound in free enzyme and in cell based assays. The crystal structure of CDK2 in complex with one of these analogues was determined and gives insight to their increased potency. The biochemical evaluation of a representative derivative is also described.


    Organizational Affiliation

    Hoffmann-La Roche Inc., 340 Kingsland St., Nutley, NJ 07110-1199, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cell division protein kinase 2
A
298Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMD
Query on FMD

Download SDF File 
Download CCD File 
A
4-((3R,4S,5R)-4-AMINO-3,5-DIHYDROXY-HEX-1-YNYL)-5-FLUORO-3-[1-(3-METHOXY-1H-PYRROL-2-YL)-METH-(Z)-YLIDENE]-1,3-DIHYDRO-INDOL-2-ONE
C20 H20 F N3 O4
RAKYKJWUUUKCCW-MPLBGYFPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FMDIC50: 3 nM BINDINGMOAD
FMDIC50: 3 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.880α = 90.00
b = 71.962β = 90.00
c = 72.779γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance