4EK4 | pdb_00004ek4

Crystal structure of the cdk2 in complex with aminopyrazole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4EK4/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: 1.26 Å
• R-Value Free: 
  0.184 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

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: 34.4 kDa 
• Atom Count: 2,740 
• Modeled Residue Count: 288 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1CK	B [auth A]	4-bromo-N-(5-methyl-1H-pyrazol-3-yl)benzamide C11 H10 Br N3 O PXLNCBTUYNESDD-UHFFFAOYSA-N
NA	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1CK	BindingDB:  4EK4	Kd: min: 4090, max: 3.32e+4 (nM) from 2 assay(s)
		-TΔS: min: -6.11e+1, max: 21.9 (kJ/mol) from 3 assay(s)
		ΔH: min: -6.19e+1, max: -1.56e+1 (kJ/mol) from 3 assay(s)
		ΔG: min: -4.00e+1, max: -2.73e+1 (kJ/mol) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free:  0.184 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.42	α = 90
b = 71.626	β = 90
c = 72.607	γ = 90

Software Package:

Software Name	Purpose
MD2	data collection
PHASER	phasing
REFMAC	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: 2013-05-08
  Changes: Database references
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary