Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 131992.73 
• Atom Count: 9047 
• Residue Count: 1148 
• Unique protein chains: 2

2WXV

Structure of CDK2-CYCLIN A with a Pyrazolo(4,3-h) quinazoline-3- carboxamide inhibitor

• DOI: 10.2210/pdb2WXV/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni, Escherichia coli BL21


• Deposited: 2009-11-10 Released: 2010-02-23 
• Deposition Author(s): Traquandi, G., Ciomei, M., Ballinari, D., Casale, E., Colombo, N., Croci, V., Fiorentini, F., Isacchi, A., Longo, A., Mercurio, C., Panzeri, A., Pastori, W., Pevarello, P., Volpi, D., Roussel, P., Vulpetti, A., Brasca, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.243 
• R-Value Work: 0.211 

Literature

Identification of Potent Pyrazolo[4,3-H]Quinazoline-3-Carboxamides as Multi-Cyclin-Dependent Kinase Inhibitors.

Traquandi, G., Ciomei, M., Ballinari, D., Casale, E., Colombo, N., Croci, V., Fiorentini, F., Isacchi, A., Longo, A., Mercurio, C., Panzeri, A., Pastori, W., Pevarello, P., Volpi, D., Roussel, P., Vulpetti, A., Brasca, M.G.

(2010) J.Med.Chem. 53: 2171

• PubMed: 20141146 
• DOI: 10.1021/jm901710h


• PubMed Abstract: 
  

Abnormal proliferation mediated by disruption of the mechanisms that keep the cell cycle under control is a hallmark of virtually all cancer cells. Compounds targeting complexes between cyclin-dependent kinases (CDKs) and cyclins (Cy) and inhibiting their activity are regarded as promising antitumor agents to complement the existing therapies. An expansion of pyrazolo[4,3-h]quinazoline chemical class oriented to the development of three points of variability was undertaken leading to a series of compounds able to inhibit CDKs both in vitro and in vivo. Starting from the CDK selective but poorly soluble hit compound 1, we succeeded in obtaining several compounds showing enhanced inhibitory activity both on CDKs and on tumor cells and displaying improved physical properties and pharmacokinetic behavior. Our study led to the identification of compound 59 as a highly potent, orally bioavailable CDK inhibitor that exhibited significant in vivo efficacy on the A2780 ovarian carcinoma xenograft model. The demonstrated mechanisms of action of compound 59 on cancer cell lines and its ability to inhibit tumor growth in vivo render this compound very interesting as potential antineoplastic agent.

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Organizational Affiliation: 

Nerviano Medical Sciences Srl, Business Unit Oncology, Viale Pasteur 10, 20014 Nerviano, MI, Italy. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CELL DIVISION PROTEIN KINASE 2	A, C	309	Homo sapiens	Mutation(s): 0  Gene Names: CDK2 (CDKN2) EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens) Go to Gene View: CDK2 Go to UniProtKB:  P24941

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
CYCLIN-A2	B, D	265	Homo sapiens	Mutation(s): 0  Gene Names: CCNA2 (CCN1, CCNA)
Find proteins for P20248 (Homo sapiens) Go to Gene View: CCNA2 Go to UniProtKB:  P20248

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
WXV	A, C	N,1-DIMETHYL-8-{[1-(METHYLSULFONYL)PIPERIDIN-4-YL]AMINO}-1H-PYRAZOLO[4,3-H]QUINAZOLINE-3-CARBOXAMIDE C18 H23 N7 O3 S MIDIIMBLQHSLFO-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
WXV	IC50: 2 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.243 
• R-Value Work: 0.211 
• Space Group: P 6₂ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 185.513	α = 90.00
b = 185.513	β = 90.00
c = 215.180	γ = 120.00

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-11-10 
• Released Date: 2010-02-23 
• Deposition Author(s): Traquandi, G., Ciomei, M., Ballinari, D., Casale, E., Colombo, N., Croci, V., Fiorentini, F., Isacchi, A., Longo, A., Mercurio, C., Panzeri, A., Pastori, W., Pevarello, P., Volpi, D., Roussel, P., Vulpetti, A., Brasca, M.G.

Revision History 

• Version 1.0: 2010-02-23
  Type: Initial release
• Version 1.1: 2011-11-09
  Type: Database references, Derived calculations, Other, Refinement description, Version format compliance