1PXJ

HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR 4-(2,4-Dimethyl-thiazol-5-yl)-pyrimidin-2-ylamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of a novel family of CDK inhibitors with the program LIDAEUS: structural basis for ligand-induced disordering of the activation loop

Wu, S.Y.McNae, I.Kontopidis, G.McClue, S.J.McInnes, C.Stewart, K.J.Wang, S.Zheleva, D.I.Marriage, H.Lane, D.P.Taylor, P.Fischer, P.M.Walkinshaw, M.D.

(2003) Structure 11: 399-410

  • Primary Citation of Related Structures:  1PW2, 1PXI, 1PXK, 1PXL

  • PubMed Abstract: 
  • A family of 4-heteroaryl-2-amino-pyrimidine CDK2 inhibitor lead compounds was discovered with the new database-mining program LIDAEUS through in silico screening. Four compounds with IC(50) values ranging from 17 to 0.9 microM were selected for X-ray ...

    A family of 4-heteroaryl-2-amino-pyrimidine CDK2 inhibitor lead compounds was discovered with the new database-mining program LIDAEUS through in silico screening. Four compounds with IC(50) values ranging from 17 to 0.9 microM were selected for X-ray crystal analysis. Two distinct binding modes are observed, one of which resembles the hydrogen bonding pattern of bound ATP. In the second binding mode, the ligands trigger a conformational change in the activation T loop by inducing movement of Lys(33) and Asp(145) side chains. The family of molecules discovered provides an excellent starting point for the design and synthesis of tight binding inhibitors, which may lead to a new class of antiproliferative drugs.


    Organizational Affiliation

    Structural Biochemistry Group, The University of Edinburgh, Michael Swann Building, King's Buildings, EH9 3JR, Edinburgh, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cell division protein kinase 2
A
298Homo sapiensGene 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
CK2
Query on CK2

Download SDF File 
Download CCD File 
A
4-(2,4-DIMETHYL-1,3-THIAZOL-5-YL)PYRIMIDIN-2-AMINE
4-(2,4-DIMETHYL-THIAZOL-5-YL)-PYRIMIDIN-2-YLAMINE
C9 H10 N4 S
CTFDMGIBHFQWKB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CK2Kd: 30300 nM (100) BINDINGDB
CK2IC50: 6500 nM (100) BINDINGDB
CK2IC50: 13000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.736α = 90.00
b = 71.704β = 90.00
c = 72.199γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance