2BPM

STRUCTURE OF CDK2-CYCLIN A WITH PHA-630529


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

3-Aminopyrazole Inhibitors of Cdk2-Cyclin a as Antitumor Agents. 2. Lead Optimization

Pevarello, P.Brasca, M.G.Orsini, P.Traquandi, G.Longo, A.Nesi, M.Orzi, F.Piutti, C.Sansonna, P.Varasi, M.Cameron, A.Vulpetti, A.Roletto, F.Alzani, R.Ciomei, M.Albanese, C.Pastori, W.Marsiglio, A.Pesenti, E.Fiorentini, F.Bischoff, J.R.Mercurio, C.

(2005) J.Med.Chem. 48: 2944

  • DOI: 10.1021/jm0408870

  • PubMed Abstract: 
  • Inhibitors of cyclin-dependent kinases (CDK) such as CDK2/cyclin A-E are currently undergoing clinical trials to verify their potential as new anticancer agents. In a previous article we described the lead discovery process of a 3-aminopyrazole class ...

    Inhibitors of cyclin-dependent kinases (CDK) such as CDK2/cyclin A-E are currently undergoing clinical trials to verify their potential as new anticancer agents. In a previous article we described the lead discovery process of a 3-aminopyrazole class of CDK2/cyclin A-E inhibitors. The endpoint of this process was PNU-292137, a compound endowed with in vivo antitumor activity in a mouse tumor xenograft model. We optimized this lead compound to improve some physicochemical properties, notably solubility and plasma protein binding. This lead optimization process brought us to the discovery of (2S)-N-(5-cyclopropyl-1H-pyrazol-3-yl)-2-[4-(2-oxo-1-pyrrolidinyl)phenyl]propanamide (PHA-533533, 13), a compound with a balanced activity vs druglike profile. Compound 13 inhibited CDK2/cyclin A with a K(i) of 31 nM, counteracting tumor cell proliferation of different cell lines with an IC(50) in the submicromolar range. Solubility was improved more than 10 times over the starting lead, while plasma protein binding was decreased from 99% to 74%. With exploitation of this globally enhanced in vitro profile, 13 was more active than PNU-292137 in vivo in the A2780 xenograft model showing a tumor growth inhibition of 70%. Proof of mechanism of action was obtained in vivo by immunohistochemical analysis of tumor slices of 13-treated vs untreated animals.


    Organizational Affiliation

    Department Chemistry, Nerviano Medical Sciences, BU-Oncology and BU-Preclinical Science, Viale Pasteur 10, 20014 Nerviano (MI), Italy. paolo.pevarello@nervianoms.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CELL DIVISION PROTEIN KINASE 2
A, C
309Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
CYCLIN A2
B, D
265Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
529
Query on 529

Download SDF File 
Download CCD File 
A, C
(2S)-N-[(3Z)-5-CYCLOPROPYL-3H-PYRAZOL-3-YLIDENE]-2-[4-(2-OXOIMIDAZOLIDIN-1-YL)PHENYL]PROPANAMIDE
C18 H19 N5 O2
JPAWNIKVRIVDBT-NABPABCNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
529IC50: 2 nM BINDINGMOAD
529IC50: 2 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.229 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 183.614α = 90.00
b = 183.614β = 90.00
c = 214.129γ = 120.00
Software Package:
Software NamePurpose
CNXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2005-12-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance