3S2P

Crystal structure of CDK2 with a 2-aminopyrimidine compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery of a novel class of 2-aminopyrimidines as CDK1 and CDK2 inhibitors

Lee, J.Kim, K.-H.Jeong, S.

(2011) Bioorg.Med.Chem.Lett. 21: 4203-4205

  • DOI: 10.1016/j.bmcl.2011.05.081

  • PubMed Abstract: 
  • A series of new 2-(2-aminopyrimidin-4-yl)phenol derivatives were synthesized as potential antitumor compounds. Substitution with pyrrolidine-3,4-diol at the 4-position of phenol provided potent inhibitory activity against CDK1 and CDK2. X-ray crystal ...

    A series of new 2-(2-aminopyrimidin-4-yl)phenol derivatives were synthesized as potential antitumor compounds. Substitution with pyrrolidine-3,4-diol at the 4-position of phenol provided potent inhibitory activity against CDK1 and CDK2. X-ray crystal structural studies were performed to account for the effect of the substituent on both the enzymatic and cell growth inhibitory activities.


    Organizational Affiliation

    Department of Chemistry, Keimyung University, Daegu 704-701, South Korea. jinho@kmu.ac.kr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent 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
PMU
Query on PMU

Download SDF File 
Download CCD File 
A
(3S,4S)-1-{3-[2-amino-6-(propan-2-yl)pyrimidin-4-yl]-4-hydroxyphenyl}pyrrolidine-3,4-diol
C17 H22 N4 O3
VIUGBRHEHAGOFV-HOTGVXAUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PMUIC50: 68 nM (100) BINDINGDB
PMUIC50: 68 nM BINDINGMOAD
PMUIC50: 68 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.777α = 90.00
b = 71.058β = 90.00
c = 72.123γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
HKL-2000data collection
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-20
    Type: Initial release