1PXL

HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR [4-(2,4-Dimethyl-thiazol-5-yl)-pyrimidin-2-yl]-(4-trifluoromethyl-phenyl)-amine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

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Ligand Structure Quality Assessment 


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

  • DOI: 10.1016/s0969-2126(03)00060-1
  • Primary Citation of Related Structures:  
    1PW2, 1PXI, 1PXJ, 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 crystal analysis ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division protein kinase 2A298Homo sapiensMutation(s): 0 
Gene Names: CDK2, CDKN2
EC: 2.7.1 (PDB Primary Data), 2.7.11.22 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
PHAROS:  P24941
GTEx:  ENSG00000123374
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CK4 (Subject of Investigation/LOI)
Query on CK4
Download Ideal Coordinates CCD File 
B [auth A]4-(2,4-DIMETHYL-1,3-THIAZOL-5-YL)-N-[4-(TRIFLUOROMETHYL)PHENYL]PYRIMIDIN-2-AMINE
C16 H13 F3 N4 S
MEZFDQUDLQCVNX-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CK4 BindingDB:  1PXL Ki: 290 (nM) from 1 assay(s)
IC50: 290 (nM) from 1 assay(s)
PDBBind:  1PXL IC50: 900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.709α = 90
b = 71.575β = 90
c = 70.429γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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