2B52 | pdb_00002b52

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

• PDB DOI: https://doi.org/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 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.228 (DCC) 

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: https://doi.org/10.1016/j.bmcl.2003.11.008
• Primary Citation 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]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.41 kDa 
• Atom Count: 2,368 
• Modeled Residue Count: 283 
• 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	298	Homo sapiens	Mutation(s): 0  Gene Names: CDK2 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
D42	B [auth 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.275 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.228 (DCC) 

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

• 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
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations