Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34417.83 
• Atom Count: 2342 
• Residue Count: 298 
• Unique protein chains: 1

5IEX

Crystal structure of (R,S)-S-{4-[(5-Bromo-4-{[(2R,3R)-2-hydroxy-1-methylpropyl]oxy}- pyrimidin-2-yl)amino]phenyl}-S-cyclopropylsulfoximide bound to CDK2

• DOI: 10.2210/pdb5IEX/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• Deposited: 2016-02-25 Released: 2016-04-27 
• Deposition Author(s): Ayaz, P., Andres, D., Kwiatkowski, D.A., Kolbe, C., Lienau, P., Siemeister, G., Luecking, U., Stegmann, C.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.254 
• R-Value Work: 0.203 

Literature

Conformational Adaption May Explain the Slow Dissociation Kinetics of Roniciclib (BAY 1000394), a Type I CDK Inhibitor with Kinetic Selectivity for CDK2 and CDK9.

Ayaz, P., Andres, D., Kwiatkowski, D.A., Kolbe, C.C., Lienau, P., Siemeister, G., Lucking, U., Stegmann, C.M.

(2016) Acs Chem.Biol. 11: 1710-1719

• PubMed: 27090615 
• DOI: 10.1021/acschembio.6b00074
• Primary Citation of Related Structures:  
  5IF1, 5IEY, 5IEV


• PubMed Abstract: 
  

Roniciclib (BAY 1000394) is a type I pan-CDK (cyclin-dependent kinase) inhibitor which has revealed potent efficacy in xenograft cancer models. Here, we show that roniciclib displays prolonged residence times on CDK2 and CDK9, whereas residence times on other CDKs are transient, thus giving rise to a kinetic selectivity of roniciclib. Surprisingly, variation of the substituent at the 5-position of the pyrimidine scaffold results in changes of up to 3 orders of magnitude of the drug-target residence time. CDK2 X-ray cocrystal structures have revealed a DFG-loop adaption for the 5-(trifluoromethyl) substituent, while for hydrogen and bromo substituents the DFG loop remains in its characteristic type I inhibitor position. In tumor cells, the prolonged residence times of roniciclib on CDK2 and CDK9 are reflected in a sustained inhibitory effect on retinoblastoma protein (RB) phosphorylation, indicating that the target residence time on CDK2 may contribute to sustained target engagement and antitumor efficacy.

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Organizational Affiliation: 

Bayer Pharma AG , Drug Discovery, Lead Discovery Berlin, Berlin, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cyclin-dependent kinase 2	A	298	Homo sapiens	Mutation(s): 0  Gene Names: CDK2 (CDKN2) EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens) Go to Gene View: CDK2 Go to UniProtKB:  P24941

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
6AF	A	(2R,3R)-3-[(5-bromo-2-{[4-(S-cyclopropylsulfonimidoyl)phenyl]amino}pyrimidin-4-yl)oxy]butan-2-ol C17 H21 Br N4 O3 S FTQAAMOHZPWVFX-KDHKCVMQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.254 
• R-Value Work: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 53.423	α = 90.00
b = 71.938	β = 90.00
c = 72.554	γ = 90.00

Software Package:

Software Name	Purpose
XSCALE	data scaling
XDS	data reduction
REFMAC	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-02-25 
• Released Date: 2016-04-27 
• Deposition Author(s): Ayaz, P., Andres, D., Kwiatkowski, D.A., Kolbe, C., Lienau, P., Siemeister, G., Luecking, U., Stegmann, C.M.

Revision History 

• Version 1.0: 2016-04-27
  Type: Initial release
• Version 1.1: 2016-05-04
  Type: Database references
• Version 1.2: 2016-06-29
  Type: Database references