Biological Assembly 1  

 3D View: Structure | 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 PQS (software)

Biological Assembly 2  

 3D View: Structure | 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 PQS (software)

Macromolecule Content

• Total Structure Weight: 131.93 kDa 
• Atom Count: 9452 
• Modelled Residue Count: 1114 
• Deposited 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: Trichoplusia ni, Escherichia coli BL21
• Mutation(s): No 


• 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: 2.40 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
• Primary Citation of Related Structures:  
  2BPM


• 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

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 GTEx:  ENSG00000123374

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 GTEx:  ENSG00000145386

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
529 (Subject of Investigation/LOI)	E [auth A], G [auth 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
SO4	F [auth A], H [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 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
b = 183.614	β = 90
c = 214.129	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Ligand Structure Quality Assessment  

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-04-03
  Changes: Data collection, Other, Source and taxonomy
• Version 1.4: 2019-10-16
  Changes: Data collection, Other