Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 131928.58 
• Atom Count: 9038 
• Residue Count: 1148 
• Unique protein chains: 2

2BPM

STRUCTURE OF CDK2-CYCLIN A WITH PHA-630529

• DOI: 10.2210/pdb2BPM/pdb

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


• Deposited: 2005-04-21 Released: 2005-12-08 
• Deposition Author(s): Cameron, A., Fogliatto, G., Pevarello, P., Brasca, M.G., Orsini, P., Traquandi, G., Longo, A., Nesi, M., Orzi, F., Piutti, C., Sansonna, P., Varasi, M., Vulpetti, A., Roletto, F., Alzani, R., Ciomei, M., Albanese, C., Pastori, W., Marsiglio, A., Pesenti, E., Fiorentini, F., Bischoff, J.R., Mercurio, C.

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Experimental Data Snapshot

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

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

• PubMed: 15828833 
• 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 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.

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Organizational Affiliation: 

Department Chemistry, Nerviano Medical Sciences, BU-Oncology and BU-Preclinical Science, 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	A, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
529	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
529	IC50: 2 nM BINDINGMOAD
529	IC50: 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 = 183.614	α = 90.00
b = 183.614	β = 90.00
c = 214.129	γ = 120.00

Software Package:

Software Name	Purpose
CNX	refinement
SCALEPACK	data scaling
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-04-21 
• Released Date: 2005-12-08 
• Deposition Author(s): Cameron, A., Fogliatto, G., Pevarello, P., Brasca, M.G., Orsini, P., Traquandi, G., Longo, A., Nesi, M., Orzi, F., Piutti, C., Sansonna, P., Varasi, M., Vulpetti, A., Roletto, F., Alzani, R., Ciomei, M., Albanese, C., Pastori, W., Marsiglio, A., Pesenti, E., Fiorentini, F., Bischoff, J.R., Mercurio, C.

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
• Version 1.3: 2019-04-03
  Type: Data collection, Other, Source and taxonomy