3S2P

Crystal structure of CDK2 with a 2-aminopyrimidine compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: https://doi.org/10.1016/j.bmcl.2011.05.081
  • Primary Citation of Related Structures:  
    3S2P

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 2298Homo sapiensMutation(s): 0 
Gene Names: CDK2
EC: 2.7.11.22
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PMU
Query on PMU

Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
PMU PDBBind:  3S2P IC50: 68 (nM) from 1 assay(s)
BindingDB:  3S2P IC50: 68 (nM) from 1 assay(s)
Binding MOAD:  3S2P IC50: 68 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.777α = 90
b = 71.058β = 90
c = 72.123γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-20
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations