2J9M

Crystal Structure of CDK2 in complex with Macrocyclic Aminopyrimidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Macrocyclic Aminopyrimidines as Multitarget Cdk and Vegf-R Inhibitors with Potent Antiproliferative Activities.

Luecking, U.Siemeister, G.Schaefer, M.Briem, H.Krueger, M.Lienau, P.Jautelat, R.

(2007) Chemmedchem 2: 63

  • DOI: 10.1002/cmdc.200600199

  • PubMed Abstract: 
  • X-ray structures from CDK2-aminopyrimidine inhibitor complexes led to the idea to stabilize the active conformation of aminopyrimidine inhibitors by incorporating the recognition site into a macrocyclic framework. A modular synthesis approach that re ...

    X-ray structures from CDK2-aminopyrimidine inhibitor complexes led to the idea to stabilize the active conformation of aminopyrimidine inhibitors by incorporating the recognition site into a macrocyclic framework. A modular synthesis approach that relies on a new late-stage macrocyclization protocol that enables fast and efficient synthesis of macrocyclic aminopyrimidines was developed. A set of structurally diverse derivatives was prepared. Macrocyclic aminopyrimidines were shown to be multitarget inhibitors of CDK1/2 and VEGF-RTKs. In addition, potent antiproliferative activities toward various human tumor cells and a human tumor xenograft model were demonstrated.


    Organizational Affiliation

    Medicinal Chemistry, Research Center Europe, Schering AG, 13342 Berlin, Germany. ulrich.luecking@schering.de




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
PY8
Query on PY8

Download SDF File 
Download CCD File 
A
6-BROMO-13-THIA-2,4,8,12,19-PENTAAZATRICYCLO[12.3.1.1~3,7~]NONADECA-1(18),3(19),4,6,14,16-HEXAENE 13,13-DIOXIDE
1(5)-BROMO-4-THIA-2,5,9-TRIAZA-1(2,4)-PYRIMIDINA-3(1,3)-BENZENACYLCLANONAPHANE-4,4-DIOXIDE
C13 H14 Br N5 O2 S
AWSQADBSXFTFKL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PY8IC50: 140 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.936α = 90.00
b = 69.934β = 90.00
c = 71.687γ = 90.00
Software Package:
Software NamePurpose
SADABSdata scaling
AMoREphasing
REFMACrefinement
SAINTdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance