2WXV

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

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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • 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 ...

    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.

    Organizational Affiliation: 

    Nerviano Medical Sciences Srl, Business Unit Oncology, Viale Pasteur 10, 20014 Nerviano, MI, Italy. gabriella.traquandi@nervianoms.com



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CELL DIVISION PROTEIN KINASE 2A, C309Homo sapiensMutation(s): 0 
Gene Names: CDK2, CDKN2
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (UniProt)
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS  P24941
GTEx  ENSG00000123374
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLIN-A2B, D265Homo sapiensMutation(s): 0 
Gene Names: CCNA2, CCN1, CCNA
Find proteins for P20248 (Homo sapiens)
Explore P20248 
Go to UniProtKB:  P20248
NIH Common Fund Data Resources
PHAROS  P20248
GTEx  ENSG00000145386
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WXV
Query on WXV
Download Ideal Coordinates CCD File 
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		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
WXVIC50 :  2   nM  PDBBind
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 = 185.513α = 90
b = 185.513β = 90
c = 215.18γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

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