3S2P | pdb_00003s2p

Crystal structure of CDK2 with a 2-aminopyrimidine compound

• PDB DOI: https://doi.org/10.2210/pdb3S2P/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-05-17 Released: 2011-07-20 
• Deposition Author(s): Kim, K.-H., Lee, J., Jeong, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.304 (Depositor), 0.294 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

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

• PubMed: 21684737 
• DOI: https://doi.org/10.1016/j.bmcl.2011.05.081
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, Keimyung University, Daegu 704-701, South Korea. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.31 kDa 
• Atom Count: 2,311 
• Modeled Residue Count: 279 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	A	298	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PMU	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.304 (Depositor), 0.294 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.777	α = 90
b = 71.058	β = 90
c = 72.123	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-20 
Deposition Author(s): Kim, K.-H., Lee, J., Jeong, S.

Revision History  

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