Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34209.76 
• Atom Count: 2445 
• Residue Count: 298 
• Unique protein chains: 1

1JVP

Crystal structure of human CDK2 (unphosphorylated) in complex with PKF049-365

• DOI: 10.2210/pdb1JVP/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• Deposited: 2001-08-31 Released: 2001-12-21 
• Deposition Author(s): Rondeau, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.253 
• R-Value Work: 0.206 

Literature

Structure-based design and protein X-ray analysis of a protein kinase inhibitor.

Furet, P., Meyer, T., Strauss, A., Raccuglia, S., Rondeau, J.M.

(2002) Bioorg.Med.Chem.Lett. 12: 221-224

• PubMed: 11755359 


• PubMed Abstract: 
  

A 5-aryl-1H-pyrazole molecular scaffold was designed to ligate the ATP binding site of cyclin dependent kinase 2 (CDK2) on the basis of crystallographic information. A search of the compound collection of Novartis using this scaffold as substructure query led to the identification of PKF049-365 as a representative of a new class of inhibitors of the cell cycle kinases CDK1/2. The three-dimensional structure of CDK2 in complex with PKF049-365 was subsequently determined by protein crystallography and refined to 1.53 A resolution. The X-ray analysis confirmed the binding mode expected from the design hypothesis. In addition, it revealed an alternative binding orientation involving a second tautomeric form of the inhibitor that was not envisaged during the design stage.

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Organizational Affiliation: 

Novartis Pharmaceuticals Inc., Oncology Research, CH-4002 Basel, Switzerland. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cell division protein kinase 2	P	298	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
LIG	P	3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE C15 H11 N3 NHOACLCXCKJMAK-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
LIG	IC50: 1600 nM BINDINGMOAD
LIG	IC50: 1600 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.253 
• R-Value Work: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 53.528	α = 90.00
b = 71.802	β = 90.00
c = 72.362	γ = 90.00

Software Package:

Software Name	Purpose
AMoRE	phasing
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-08-31 
• Released Date: 2001-12-21 
• Deposition Author(s): Rondeau, J.M.

Revision History 

• Version 1.0: 2001-12-21
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance