Biological Assembly 1  

 3D View: Structure | 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: 34.30 kDa 
• Atom Count: 2575 
• Modelled Residue Count: 294 
• Deposited Residue Count: 298 
• Unique protein chains: 1

1PXO

HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR [4-(2-Amino-4-methyl-thiazol-5-yl)-pyrimidin-2-yl]-(3-nitro-phenyl)-amine

• DOI: 10.2210/pdb1PXO/pdb

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


• Deposited: 2003-07-04 Released: 2004-04-13 
• Deposition Author(s): Wang, S., Meades, C., Wood, G., Osnowski, A., Anderson, S., Yuill, R., Thomas, M., Mezna, M., Jackson, W., Midgley, C., Griffiths, G., McNae, I., Wu, S.Y., McInnes, C., Zheleva, D., Walkinshaw, M.D., Fischer, P.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.235 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 

Literature

2-Anilino-4-(thiazol-5-yl)pyrimidine CDK inhibitors: synthesis, SAR analysis, X-ray crystallography, and biological activity.

Wang, S., Meades, C., Wood, G., Osnowski, A., Anderson, S., Yuill, R., Thomas, M., Mezna, M., Jackson, W., Midgley, C., Griffiths, G., Fleming, I., Green, S., McNae, I., Wu, S.Y., McInnes, C., Zheleva, D., Walkinshaw, M.D., Fischer, P.M.

(2004) J Med Chem 47: 1662-1675

• PubMed: 15027857 
• DOI: 10.1021/jm0309957
• Primary Citation of Related Structures:  
  1PXM, 1PXN, 1PXO, 1PXP


• PubMed Abstract: 
  

Following the identification through virtual screening of 4-(2,4-dimethyl-thiazol-5-yl)pyrimidin-2-ylamines as moderately potent inhibitors of cyclin-dependent kinase-2 (CDK2), a CDK inhibitor analogue program was initiated. The first aims were to optimize potency and to evaluate the cellular mode of action of lead candidate molecules. Here the synthetic chemistry, the structure-guided design approach, and the structure-activity relationships (SARs) that led to the discovery of 2-anilino-4-(thiazol-5-yl)pyrimidine ATP-antagonistic CDK2 inhibitors, many with very low nM K(i)s against CDK2, are reported. Furthermore, X-ray crystal structures of four representative analogues from our chemical series in complex with CDK2 are presented, and these structures are used to rationalize the observed biochemical SARs. Finally results are reported that show, using the most potent CDK2 inhibitor compound from the current series, that the observed antiproliferative and proapoptotic effects are consistent with cellular CDK2 and CDK9 inhibition.

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Related Citations: 

• 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

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Organizational Affiliation: 

Cyclacel Limited, James Lindsay Place, Dundee DD1 5JJ, Scotland, UK.

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 GTEx:  ENSG00000123374

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CK7 (Subject of Investigation/LOI)	B [auth A]	[4-(2-AMINO-4-METHYL-THIAZOL-5-YL)-PYRIMIDIN-2-YL]-(3-NITRO-PHENYL)-AMINE C14 H12 N6 O2 S DYTKVFHLKPDNRW-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CK7	PDBBind:  1PXO	Ki: 2 (nM) from 1 assay(s)
	BindingDB:  1PXO	Ki: 2 (nM) from 1 assay(s)
	Binding MOAD:  1PXO	Ki: 2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.235 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.489	α = 90
b = 71.987	β = 90
c = 72.362	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-07-04 
• Released Date: 2004-04-13 
Deposition Author(s): Wang, S., Meades, C., Wood, G., Osnowski, A., Anderson, S., Yuill, R., Thomas, M., Mezna, M., Jackson, W., Midgley, C., Griffiths, G., McNae, I., Wu, S.Y., McInnes, C., Zheleva, D., Walkinshaw, M.D., Fischer, P.M.

Revision History  

• Version 1.0: 2004-04-13
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance