3NS9

Crystal structure of CDK2 in complex with inhibitor BS-194

• PDB DOI:  https://doi.org/10.2210/pdb3NS9/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-07-01 Released: 2010-12-08 
• Deposition Author(s): Hazel, P., Freemont, P.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.265 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 

Literature

A Novel Pyrazolo[1,5-a]pyrimidine Is a Potent Inhibitor of Cyclin-Dependent Protein Kinases 1, 2, and 9, Which Demonstrates Antitumor Effects in Human Tumor Xenografts Following Oral Administration.

Heathcote, D.A., Patel, H., Kroll, S.H., Hazel, P., Periyasamy, M., Alikian, M., Kanneganti, S.K., Jogalekar, A.S., Scheiper, B., Barbazanges, M., Blum, A., Brackow, J., Siwicka, A., Pace, R.D., Fuchter, M.J., Snyder, J.P., Liotta, D.C., Freemont, P.S., Aboagye, E.O., Coombes, R.C., Barrett, A.G., Ali, S.

(2010) J Med Chem 53: 8508-8522

• PubMed: 21080703 
• DOI: https://doi.org/10.1021/jm100732t
• Primary Citation of Related Structures:  
  3NS9


• PubMed Abstract: 
  

Cyclin-dependent protein kinases (CDKs) are central to the appropriate regulation of cell proliferation, apoptosis, and gene expression. Abnormalities in CDK activity and regulation are common features of cancer, making CDK family members attractive targets for the development of anticancer drugs. Here, we report the identification of a pyrazolo[1,5-a]pyrimidine derived compound, 4k (BS-194), as a selective and potent CDK inhibitor, which inhibits CDK2, CDK1, CDK5, CDK7, and CDK9 (IC₅₀= 3, 30, 30, 250, and 90 nmol/L, respectively). Cell-based studies showed inhibition of the phosphorylation of CDK substrates, Rb and the RNA polymerase II C-terminal domain, down-regulation of cyclins A, E, and D1, and cell cycle block in the S and G₂/M phases. Consistent with these findings, 4k demonstrated potent antiproliferative activity in 60 cancer cell lines tested (mean GI₅₀= 280 nmol/L). Pharmacokinetic studies showed that 4k is orally bioavailable, with an elimination half-life of 178 min following oral dosing in mice. When administered at a concentration of 25 mg/kg orally, 4k inhibited human tumor xenografts and suppressed CDK substrate phosphorylation. These findings identify 4k as a novel, potent CDK selective inhibitor with potential for oral delivery in cancer patients.

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Organizational Affiliation: 

Dept of Oncology, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, England.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 34.36 kDa 
• Atom Count: 2,552 
• Modelled Residue Count: 289 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein kinase 2	A	298	Homo sapiens	Mutation(s): 0  Gene Names: CDK2, CDKN2 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NS9	B [auth A]	(2S,3S)-3-{[7-(benzylamino)-3-(1-methylethyl)pyrazolo[1,5-a]pyrimidin-5-yl]amino}butane-1,2,4-triol C20 H27 N5 O3 KRIWIRSMQRQYJG-DLBZAZTESA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NS9	Binding MOAD:  3NS9	IC50: 3 (nM) from 1 assay(s)
	PDBBind:  3NS9	IC50: 3 (nM) from 1 assay(s)
	BindingDB:  3NS9	IC50: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.265 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.05	α = 90
b = 70.69	β = 90
c = 72.11	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-08 
Deposition Author(s): Hazel, P., Freemont, P.S.

Revision History  

• Version 1.0: 2010-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description