Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.33 kDa 
• Atom Count: 2397 
• Modelled Residue Count: 290 
• Deposited Residue Count: 298 
• Unique protein chains: 1

1PXL

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

• PDB DOI: 10.2210/pdb1PXL/pdb

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


• Deposited: 2003-07-04 Released: 2003-12-09 
• Deposition Author(s): 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.

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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 

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

• PubMed: 12679018 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein kinase 2	A	298	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CK4	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

Binding Affinity Annotations
ID	Source	Binding 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 = 52.709	α = 90
b = 71.575	β = 90
c = 70.429	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-07-04 
• Released Date: 2003-12-09 
Deposition Author(s): 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.

Revision History  

• 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