2CLX

4-Arylazo-3,5-diamino-1H-pyrazole CDK Inhibitors: SAR Study, Crystal Structure in Complex with CDK2, Selectivity, and Cellular Effects


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

4-Arylazo-3,5-Diamino-1H-Pyrazole Cdk Inhibitors: Sar Study, Crystal Structure in Complex with Cdk2, Selectivity, and Cellular Effects

Krystof, V.Cankar, P.Frysova, I.Slouka, J.Kontopidis, G.Dzubak, P.Hajduch, M.De Azevedo Junior, W.F.Paprskarova, M.Orsag, M.Rolcik, J.Latr, A.Fischer, P.M.Strnad, M.

(2006) J Med Chem 49: 6500

  • DOI: 10.1021/jm0605740
  • Primary Citation of Related Structures:  
    2CLX

  • PubMed Abstract: 
  • In a routine screening of our small-molecule compound collection we recently identified 4-arylazo-3,5-diamino-1H-pyrazoles as a novel group of ATP antagonists with moderate potency against CDK2-cyclin E. A preliminary SAR study based on 35 analogues ...

    In a routine screening of our small-molecule compound collection we recently identified 4-arylazo-3,5-diamino-1H-pyrazoles as a novel group of ATP antagonists with moderate potency against CDK2-cyclin E. A preliminary SAR study based on 35 analogues suggests ways in which the pharmacophore could be further optimized, for example, via substitutions in the 4-aryl ring. Enzyme kinetics studies with the lead compound and X-ray crystallography of an inhibitor-CDK2 complex demonstrated that its mode of inhibition is competitive. Functional kinase assays confirmed the selectivity toward CDKs, with a preference for CDK9-cyclin T1. The most potent inhibitor, 4-[(3,5-diamino-1H-pyrazol-4-yl)diazenyl]phenol 31b (CAN508), reduced the frequency of S-phase cells of the cancer cell line HT-29 in antiproliferation assays. Further observed cellular effects included decreased phosphorylation of the retinoblastoma protein and the C-terminal domain of RNA polymerase II, inhibition of mRNA synthesis, and induction of the tumor suppressor protein p53, all of which are consistent with inhibition of CDK9.


    Organizational Affiliation

    Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, Slechtitelů 11, 783 71 Olomouc, Czech Republic.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CELL DIVISION PROTEIN KINASE 2A298Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (PDB Primary Data)
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS  P24941
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F18
Query on F18

Download CCD File 
A
4-[(E)-(3,5-DIAMINO-1H-PYRAZOL-4-YL)DIAZENYL]PHENOL
C9 H10 N6 O
AYZRKFOEZQBUEA-SEYXRHQNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F18IC50:  20000   nM  BindingDB
F18Ki:  69000   nM  BindingDB
F18Ki :  13300   nM  PDBBind
F18IC50:  69000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.37α = 90
b = 70.75β = 90
c = 72.18γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-01-30
    Changes: Data collection, Experimental preparation, Other