1JVP | pdb_00001jvp

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

• PDB DOI: https://doi.org/10.2210/pdb1JVP/pdb

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


• 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 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

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 
• DOI: https://doi.org/10.1016/s0960-894x(01)00715-6
• Primary Citation of Related Structures:  
  1JVP


• 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]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.21 kDa 
• Atom Count: 2,709 
• Modelled Residue Count: 281 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein kinase 2	A [auth P]	298	Homo sapiens	Mutation(s): 0  EC: 2.7.1.37 (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
89E	B [auth P]	3-pyridin-4-yl-2,4-dihydroindeno[1,2-c]pyrazole C15 H11 N3 NHOACLCXCKJMAK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.253 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.528	α = 90
b = 71.802	β = 90
c = 72.362	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2021-09-22
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-02-07
  Changes: Data collection