3EJ1 | pdb_00003ej1

CDK2/CyclinA complexed with a pyrazolopyridazine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3EJ1/pdb

• Classification: Transferase/Cell cycle
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-17 Released: 2008-10-21 
• Deposition Author(s): Stevens, K., Reno, M., Alberti, J., Price, D., Kane-Carson, L., Knick, V., Shewchuk, L., Hassell, A., Veal, J., Peel, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.22 Å
• R-Value Free: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Synthesis and evaluation of pyrazolo[1,5-b]pyridazines as selective cyclin dependent kinase inhibitors.

Stevens, K.L., Reno, M.J., Alberti, J.B., Price, D.J., Kane-Carson, L.S., Knick, V.B., Shewchuk, L.M., Hassell, A.M., Veal, J.M., Davis, S.T., Griffin, R.J., Peel, M.R.

(2008) Bioorg Med Chem Lett 18: 5758-5762

• PubMed: 18835709 
• DOI: https://doi.org/10.1016/j.bmcl.2008.09.069
• Primary Citation of Related Structures:  
  3EID, 3EJ1


• PubMed Abstract: 
  

  A novel series of pyrazolo[1,5-b]pyridazines have been synthesized and identified as cyclin dependant kinase inhibitors potentially useful for the treatment of solid tumors. Modification of the hinge-binding amine or the C(2)- and C(6)-substitutions on the pyrazolopyridazine core provided potent inhibitors of CDK4 and demonstrated enzyme selectivity against VEGFR-2 and GSK3beta.

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Organizational Affiliation: 

Department of Oncology, GlaxoSmithKline, Research Triangle Park, NC 27709, USA. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 128.19 kDa 
• Atom Count: 8,826 
• Modelled Residue Count: 1,104 
• Deposited Residue Count: 1,116 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein kinase 2	A, C	298	Homo sapiens	Mutation(s): 0  Gene Names: CDK2 EC: 2.7.11.22
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	260	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5BP	E [auth A], F [auth C]	N-cyclopropyl-4-pyrazolo[1,5-b]pyridazin-3-ylpyrimidin-2-amine C13 H12 N6 CAGHIASAHLPQMS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5BP	BindingDB:  3EJ1	IC50: 120 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.22 Å
• R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.776	α = 90
b = 183.776	β = 90
c = 214.045	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-21 
Deposition Author(s): Stevens, K., Reno, M., Alberti, J., Price, D., Kane-Carson, L., Knick, V., Shewchuk, L., Hassell, A., Veal, J., Peel, M.

Revision History  

• Version 1.0: 2008-10-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description