Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 131.99 kDa 
• Atom Count: 9187 
• Modelled Residue Count: 1115 
• Deposited Residue Count: 1148 
• Unique protein chains: 2

2WXV

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

• PDB DOI: 10.2210/pdb2WXV/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni, Escherichia coli BL21
• Mutation(s): No 


• 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: 2.60 Å
• R-Value Free: 0.243 
• R-Value Work: 0.211 
• R-Value Observed: 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
• Primary Citation of Related Structures:  
  2WXV


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELL DIVISION PROTEIN KINASE 2	A, C	309	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLIN-A2	B, D	265	Homo sapiens	Mutation(s): 0  Gene Names: CCNA2, CCN1, CCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P20248 (Homo sapiens) Explore P20248  Go to UniProtKB:  P20248
PHAROS:  P20248

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WXV	E [auth A], F [auth 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
SO4	G [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
WXV	PDBBind:  2WXV	IC50: 2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.243 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.513	α = 90
b = 185.513	β = 90
c = 215.18	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

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
  Changes: Database references, Derived calculations, Other, Refinement description, Version format compliance
• Version 1.2: 2019-04-03
  Changes: Data collection, Other, Source and taxonomy