4LYN

Crystal structure of cyclin-dependent kinase 2 (cdk2-wt) complex with (2s)-n-(5-(((5-tert-butyl-1,3-oxazol-2-yl)methyl)sulfanyl)-1,3-thiazol-2-yl)-2-phenylpropanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of Aminothiazole Inhibitors of Cyclin-Dependent Kinase 2: Synthesis, X-Ray Crystallographic Analysis, and Biological Activities

Kim, K.S.Kimball, S.D.Misra, R.N.Rawlins, D.B.Hunt, J.T.Xiao, H.-Y.Lu, S.Qian, L.Han, W.C.Shan, W.Mitt, T.Cai, Z.-W.Poss, M.A.Zhu, H.Sack, J.S.Tokarski, J.S.Chang, C.Y.Pavletich, N.Kamath, A.Humphreys, W.G.Marathe, P.Bursuker, I.Kellar, K.A.Roongta, U.Batorsky, R.Mulheron, J.G.Bol, D.Fairchild, C.R.Lee, F.Y.Webster, K.R.

(2002) J.Med.Chem. 45: 3905-3927


  • PubMed Abstract: 
  • High throughput screening identified 2-acetamido-thiazolylthio acetic ester 1 as an inhibitor of cyclin-dependent kinase 2 (CDK2). Because this compound is inactive in cells and unstable in plasma, we have stabilized it to metabolic hydrolysis by rep ...

    High throughput screening identified 2-acetamido-thiazolylthio acetic ester 1 as an inhibitor of cyclin-dependent kinase 2 (CDK2). Because this compound is inactive in cells and unstable in plasma, we have stabilized it to metabolic hydrolysis by replacing the ester moiety with a 5-ethyl-substituted oxazole as in compound 14. Combinatorial and parallel synthesis provided a rapid analysis of the structure-activity relationship (SAR) for these inhibitors of CDK2, and over 100 analogues with IC(50) values in the 1-10 nM range were rapidly prepared. The X-ray crystallographic data of the inhibitors bound to the active site of CDK2 protein provided insight into the binding modes of these inhibitors, and the SAR of this series of analogues was rationalized. Many of these analogues displayed potent and broad spectrum antiproliferative activity across a panel of tumor cell lines in vitro. In addition, A2780 ovarian carcinoma cells undergo rapid apoptosis following exposure to CDK2 inhibitors of this class. Mechanism of action studies have confirmed that the phosphorylation of CDK2 substrates such as RB, histone H1, and DNA polymerase alpha (p70 subunit) is reduced in the presence of compound 14. Further optimization led to compounds such as water soluble 45, which possesses a favorable pharmacokinetic profile in mice and demonstrates significant antitumor activity in vivo in several murine and human models, including an engineered murine mammary tumor that overexpresses cyclin E, the coactivator of CDK2.


    Organizational Affiliation

    Department of Oncology Chemistry, Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, New Jersey 08543-4000, USA. kyoung.kim@bms.com




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
1YG
Query on 1YG

Download SDF File 
Download CCD File 
A
(2S)-N-(5-{[(5-tert-butyl-1,3-oxazol-2-yl)methyl]sulfanyl}-1,3-thiazol-2-yl)-2-phenylpropanamide
C20 H23 N3 O2 S2
FIZSPBCJAWUURL-ZDUSSCGKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1YGIC50: 60 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.460α = 90.00
b = 71.840β = 90.00
c = 72.190γ = 90.00
Software Package:
Software NamePurpose
X-GENdata reduction
BUSTERrefinement
AMoREphasing
X-GENdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-07-31 
  • Released Date: 2013-10-02 
  • Deposition Author(s): Sack, J.S.

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description
  • Version 1.2: 2018-01-24
    Type: Database references