4EK8 | pdb_00004ek8

Crystal structure of the cdk2 in complex with thiazolylpyrimidine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4EK8/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2012-04-09 Released: 2013-05-01 
• Deposition Author(s): Kang, Y.N., Stuckey, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.215 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Crystal structure of the cdk2 in complex with thiazolylpyrimidine inhibitor

Kang, Y.N., Stuckey, J.A.

To be published.

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: 34.33 kDa 
• Atom Count: 2,547 
• Modelled Residue Count: 282 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	A	299	Homo sapiens	Mutation(s): 1  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 GTEx:  ENSG00000123374

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
16K	B [auth A]	4-(2,4-dimethyl-1,3-thiazol-5-yl)-N-(3-nitrophenyl)pyrimidin-2-amine C15 H13 N5 O2 S DEIGLICSSNUYPO-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
16K	BindingDB:  4EK8	Ki: 110 (nM) from 1 assay(s)
		Kd: min: 72.7, max: 4380 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.215 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.42	α = 90
b = 71.879	β = 90
c = 72.417	γ = 90

Software Package:

Software Name	Purpose
MD2	data collection
PHASER	phasing
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-01 
Deposition Author(s): Kang, Y.N., Stuckey, J.A.

Revision History  

• Version 1.0: 2013-05-01
  Type: Initial release
  
• Version 1.1: 2013-05-22
  Changes: Other
• Version 1.2: 2013-05-29
  Changes: Other
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary