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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/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. eddyyue@incyte.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division protein kinase 2298Homo sapiensMutation(s): 0 
Gene Names: CDK2
EC: 2.7.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
PHAROS:  P24941
GTEx:  ENSG00000123374 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24941
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / 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
Binding Affinity Annotations 
IDSourceBinding Affinity
D42 BindingDB:  2B52 IC50: 8 (nM) from 1 assay(s)
PDBBind:  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

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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