2CLX

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

• PDB DOI:  https://doi.org/10.2210/pdb2CLX/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2006-05-02 Released: 2006-11-01 
• Deposition Author(s): Krystof, V., Cankar, P., Frysova, I., Slouka, J., Kontopidis, G., Dzubak, P., Hajduch, M., Deazevedo, W.F., Paprskarova, M., Orsag, M., Rolcik, J., Latr, A., Fischer, P.M., Strnad, M.

---

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 

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

• PubMed: 17064068 
• DOI: https://doi.org/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 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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 34.19 kDa 
• Atom Count: 2,638 
• Modelled Residue Count: 293 
• 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, CDKN2 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens) Explore P24941  Go to UniProtKB:  P24941
PHAROS:  P24941

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F18	B [auth A]	4-[(E)-(3,5-DIAMINO-1H-PYRAZOL-4-YL)DIAZENYL]PHENOL C9 H10 N6 O AYZRKFOEZQBUEA-SEYXRHQNSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
F18	BindingDB:  2CLX	Ki: 6.90e+4 (nM) from 1 assay(s)
		IC50: min: 2.00e+4, max: 6.90e+4 (nM) from 2 assay(s)
	PDBBind:  2CLX	Ki: 1.33e+4 (nM) from 1 assay(s)

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 = 53.37	α = 90
b = 70.75	β = 90
c = 72.18	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-01 
Deposition Author(s): Krystof, V., Cankar, P., Frysova, I., Slouka, J., Kontopidis, G., Dzubak, P., Hajduch, M., Deazevedo, W.F., Paprskarova, M., Orsag, M., Rolcik, J., Latr, A., Fischer, P.M., Strnad, M.

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