2BTR

STRUCTURE OF CDK2 COMPLEXED WITH PNU-198873

• PDB DOI: https://doi.org/10.2210/pdb2BTR/pdb

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


• Deposited: 2005-06-06 Released: 2005-11-09 
• Deposition Author(s): Vulpetti, A., Casale, E., Roletto, F., Amici, R., Villa, M., Pevarello, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.272 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 

Literature

Structure-Based Drug Design to the Discovery of New 2-Aminothiazole Cdk2 Inhibitors.

Vulpetti, A., Casale, E., Roletto, F., Amici, R., Villa, M., Pevarello, P.

(2006) J Mol Graph Model 24: 341

• PubMed: 16260160 
• DOI: https://doi.org/10.1016/j.jmgm.2005.09.012
• Primary Citation of Related Structures:  
  2BTR, 2BTS


• PubMed Abstract: 
  

  N-(5-Bromo-1,3-thiazol-2-yl)butanamide (compound 1) was found active (IC50=808 nM) in a high throughput screening (HTS) for CDK2 inhibitors. By exploiting crystal structures of several complexes between CDK2 and inhibitors and applying structure-based drug design (SBDD), we rapidly discovered a very potent and selective CDK2 inhibitor 4-[(5-isopropyl-1,3-thiazol-2-yl)amino] benzenesulfonamide (compound 4, IC50=20 nM). The syntheses, structure-based analog design, kinases inhibition data and X-ray crystallographic structures of CDK2/inhibitor complexes are reported.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 34.24 kDa 
• Atom Count: 2,300 
• Modelled Residue Count: 275 
• 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  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U73	B [auth A]	N-(5-ISOPROPYL-THIAZOL-2-YL)-2-PYRIDIN-3-YL-ACETAMIDE C13 H15 N3 O S WQZOOPQQADNJEG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
U73	PDBBind:  2BTR	IC50: 95 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.272 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.215	α = 90
b = 71.615	β = 90
c = 71.588	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-09 
Deposition Author(s): Vulpetti, A., Casale, E., Roletto, F., Amici, R., Villa, M., Pevarello, P.

Revision History  

• Version 1.0: 2005-11-09
  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, Derived calculations, Other