4EK6

Crystal structure of the cdk2 in complex with aminopyrazole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4EK6/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: 1.52 Å
• R-Value Free: 0.217 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

Literature

Crystal structure of the cdk2 in complex with aminopyrazole 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: 2,614 
• Modelled Residue Count: 279 
• 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
10K	B [auth A]	N-(3-cyclopropyl-1H-pyrazol-5-yl)-2-[4-(thiophen-2-yl)phenyl]acetamide C18 H17 N3 O S LQBKAYJFACGUCC-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
10K	BindingDB:  4EK6	Kd: min: 79, max: 4960 (nM) from 3 assay(s)
		IC50: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.217 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.328	α = 90
b = 71.647	β = 90
c = 72.332	γ = 90

Software Package:

Software Name	Purpose
MD2	data collection
PHASER	phasing
BUSTER	refinement
HKL-2000	data reduction
DENZO	data reduction
SCALEPACK	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: 2013-05-08
  Changes: Database references
• Version 1.2: 2013-05-29
  Changes: Other
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary