Biological Assembly 1  

 3D View: Structure | 1D-3D View | 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: 34.40 kDa 
• Atom Count: 2353 
• Modelled Residue Count: 276 
• Deposited Residue Count: 298 
• Unique protein chains: 1

2B55

Human cyclin dependent kinase 2 (cdk2) complexed with indenopyraxole DIN-101312

• PDB DOI: 10.2210/pdb2B55/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: 1.85 Å
• R-Value Free: 0.256 
• R-Value Work: 0.213 

Literature

Synthesis and Evaluation of Indenopyrazoles as Cyclin-Dependent Kinase Inhibitors. 3. Structure Activity Relationships at C3

Yue, E.W., Higley, C.A., Dimeo, S.V., Carini, D.J., Nugiel, D.A., Benware, C., Benfield, P.A., Cox, S., Burton, C.R., Grafstrom, R.H., Sharp, D.M., Sisk, L.M., Boylan, J.F., Muckelbauer, J.K., Smallwood, A.M., Chen, H., Chang, C.-H., Seitz, S.P., Trainor, G.L.

(2002) J Med Chem 45: 5233-5248

• PubMed: 12431051 
• DOI: 10.1021/jm0201722
• Primary Citation of Related Structures:  
  2B55


• PubMed Abstract: 
  

The identification of indeno[1,2-c]pyrazol-4-ones as inhibitors of cyclin-dependent kinases (CDKs) has led to the discovery of a series of novel and potent compounds. Herein, we report the effects of substitutions at C3 of the indeno[1,2-c]pyrazol-4-one core with alkyls, heterocycles, and substituted phenyls. Substitutions at the para position of the phenyl ring at C3 were generally well-tolerated; however, larger groups were generally inactive. For alkyls directly attached to C3, longer chain substituents were not tolerated; however, shorter alkyl groups and cyclic alkyls were acceptable. In general, the heterocycles at C3 gave the most potent analogues. One such heterocycle, 24j, was examined in detail and was determined to have a biological profile consistent with CDK inhibition. An X-ray crystal structure of one of the alkyl compounds, 13q, complexed with CDK2 was determined and showed the inhibitor residing in the adenosine 5'-triphosphate pocket of the enzyme.

---

Organizational Affiliation: 

Bristol-Myers Squibb Company, Experimental Station, P.O. Box 80500, Wilmington, Delaware 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)
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
D31	B [auth A]	2-(4-(AMINOMETHYL)PIPERIDIN-1-YL)-N-(3_CYCLOHEXYL-4-OXO-2,4-DIHYDROINDENO[1,2-C]PYRAZOL-5-YL)ACETAMIDE C24 H31 N5 O2 AITZHKQVQNLKHI-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
D31	BindingDB:  2B55	IC50: 96 (nM) from 1 assay(s)
	PDBBind:  2B55	IC50: 96 (nM) from 1 assay(s)
	Binding MOAD:  2B55	IC50: 96 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.256 
• R-Value Work: 0.213 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.98	α = 90
b = 72.2	β = 90
c = 53.52	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