2B52

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

Experimental Data Snapshot

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

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This is version 1.2 of the entry. See complete history. 


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

  • 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 ...

    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. eddyyue@incyte.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division protein kinase 2A298Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24941
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D42
Query on D42
Download Ideal Coordinates CCD File 
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		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
D42 PDBBind:  2B52 IC50: 8 (nM) from 1 assay(s)
BindingDB:  2B52 IC50: 8 (nM) from 1 assay(s)
Binding MOAD:  2B52 IC50: 8 (nM) from 1 assay(s)
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 = 72.03α = 90
b = 72.01β = 90
c = 53.5γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • 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