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 

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Ligand Structure Quality Assessment 


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
  • 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 2A298Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PMU (Subject of Investigation/LOI)
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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
PMU BindingDB:  3S2P IC50: 68 (nM) from 1 assay(s)
Binding MOAD:  3S2P IC50: 68 (nM) from 1 assay(s)
PDBBind:  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