2BKZ

STRUCTURE OF CDK2-CYCLIN A WITH PHA-404611

• PDB DOI: https://doi.org/10.2210/pdb2BKZ/pdb

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


• Deposited: 2005-02-23 Released: 2006-03-08 
• Deposition Author(s): DAlessio, R., Bargiottia, A., Metz, S., Brasca, M.G., Cameron, A., Ermoli, A., Marsiglio, A., Polucci, P., Roletto, F., Tibolla, M., Vazquez, M.L., Vulpetti, A., Pevarello, P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.259 
• R-Value Work: 0.230 

Literature

Benzodipyrazoles: A New Class of Potent Cdk2 Inhibitors

Dalessio, R., Bargiottia, A., Metz, S., Brasca, M.G., Cameron, A., Ermoli, A., Marsiglio, A., Polucci, P., Roletto, F., Tibolla, M., Vazquez, M.L., Vulpetti, A., Pevarello, P.

(2005) Bioorg Med Chem Lett 15: 1315

• PubMed: 15713378 
• DOI: https://doi.org/10.1016/j.bmcl.2005.01.023
• Primary Citation of Related Structures:  
  2BKZ


• PubMed Abstract: 
  

  The synthesis and the preliminary expansion of this new class of CDK2 inhibitors are presented. The synthesis was accomplished using a solution-phase protocol amenable to rapid parallel expansion and suitable to be scaled-up in view of possible lead development. Following a medicinal chemistry program aimed at improving cell permeability and selectivity, a series of compounds with nanomolar activity in the biochemical assay and able to efficiently inhibit tumor cell proliferation has been obtained.

---

Organizational Affiliation: 

Chemistry Department, Nerviano Medical Sciences, Oncology Business Unit, Viale Pasteur 10, 20014 Nerviano (MI), Italy. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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: 131.97 kDa 
• Atom Count: 9,295 
• Modelled Residue Count: 1,112 
• Deposited Residue Count: 1,148 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELL DIVISION PROTEIN KINASE 2	A, C	309	Homo sapiens	Mutation(s): 0  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
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
SBC	E [auth A], G [auth C]	1-[4-(AMINOSULFONYL)PHENYL]-1,6-DIHYDROPYRAZOLO[3,4-E]INDAZOLE-3-CARBOXAMIDE C15 H12 N6 O3 S HGAKLLFPOGATII-UHFFFAOYSA-N
SO4	F [auth A], H [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
SBC	BindingDB:  2BKZ	IC50: 0.3 (nM) from 1 assay(s)
	PDBBind:  2BKZ	IC50: 7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.259 
• R-Value Work: 0.230 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.862	α = 90
b = 183.862	β = 90
c = 214.572	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-08 
Deposition Author(s): DAlessio, R., Bargiottia, A., Metz, S., Brasca, M.G., Cameron, A., Ermoli, A., Marsiglio, A., Polucci, P., Roletto, F., Tibolla, M., Vazquez, M.L., Vulpetti, A., Pevarello, P.

Revision History  

• Version 1.0: 2006-03-08
  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: 2024-05-08
  Changes: Data collection, Database references, Other