3EID | pdb_00003eid

CDK2/CyclinA complexed with a pyrazolopyridazine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3EID/pdb

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


• Deposited: 2008-09-15 Released: 2008-10-21 
• Deposition Author(s): Steven, 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: 3.15 Å
• R-Value Free: 
  0.261 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.204 (Depositor) 
• R-Value Observed: 
  0.207 (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 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: 128.18 kDa 
• Atom Count: 8,755 
• Modeled Residue Count: 1,094 
• 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
PO5	E [auth A]	(2S)-1-(dimethylamino)-3-(4-{[4-(6-morpholin-4-ylpyrazolo[1,5-b]pyridazin-3-yl)pyrimidin-2-yl]amino}phenoxy)propan-2-ol C25 H30 N8 O3 GBRORGYPYNNDGL-IBGZPJMESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.261 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.204 (Depositor) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.506	α = 90
b = 184.506	β = 90
c = 213.302	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-21 
Deposition Author(s): Steven, 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