Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.41 kDa 
• Atom Count: 2368 
• Residue Count: 283 
• Unique protein chains: 1

2B52

Human cyclin dependent kinase 2 (CDK2) complexed with DPH-042562

• DOI: 10.2210/pdb2B52/pdb

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


• Deposited: 2005-09-27 Released: 2005-10-11 
• Deposition Author(s): Muckelbauer, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.275 
• R-Value Work: 0.219 

Literature

Synthesis and Evaluation of Indenopyrazoles as Cyclin-Dependent Kinase Inhibitors. Part 4: Heterocycles at C3

Yue, E.W., Dimeo, S.V., Higley, C.A., Markwalder, J.A., Burton, C.R., Benfield, P.A., Grafstrom, R.H., Cox, S., Muckelbauer, J.K., Smallwood, A., Chen, H., Chang, C.-H., Trainor, G.L., Seitz, S.P.

(2004) Bioorg Med Chem Lett 14: 343-346

• PubMed: 14698155 
• DOI: 10.1016/j.bmcl.2003.11.008
• Primary Citation of Related Structures:  
  2B52


• PubMed Abstract: 
  

New indeno[1,2-c]pyrazol-4-one cyclin dependent kinase inhibitors have been disclosed. The most promising compounds are nanomolar enzyme inhibitors with excellent activity against tumor cells. The most advanced compound retains cell culture activity even in the presence of human serum proteins. The most advanced compound did not kill the normal fibroblast line AG1523.

---

Organizational Affiliation: 

Bristol-Myers Squibb Company, Experimental Station, PO Box 80500, Wilmington, DE 19880-0500, USA. [e-mail]

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: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (UniProt)
Find proteins for P24941 (Homo sapiens) Explore P24941  Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS  P24941 GTEx  ENSG00000123374

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D42	A	1-(3-(2,4-DIMETHYLTHIAZOL-5-YL)-4-OXO-2,4-DIHYDROINDENO[1,2-C]PYRAZOL-5-YL)-3-(4-METHYLPIPERAZIN-1-YL)UREA C21 H23 N7 O2 S KRKQVGZXTNLQSV-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
D42	IC50:  8   nM  BindingDB
D42	IC50:  8   nM  Binding MOAD
D42	IC50 :  8   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.275 
• R-Value Work: 0.219 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.03	α = 90
b = 72.01	β = 90
c = 53.5	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-09-27 
• Released Date: 2005-10-11 
Deposition Author(s): Muckelbauer, J.

Revision History 

• Version 1.0: 2005-10-11
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance