3SW4

Crystal Structure of the CDK2 in complex with thiazolylpyrimidine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3SW4/pdb

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


• Deposited: 2011-07-13 Released: 2012-08-01 
• 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: 0.208 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 

Literature

Crystal Structure of the CDK2 in complex with a 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: 34.39 kDa 
• Atom Count: 2,499 
• Modelled Residue Count: 281 
• 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 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
18K	B [auth A]	N'-[4-(2-amino-4-methyl-1,3-thiazol-5-yl)pyrimidin-2-yl]-N,N-dimethylbenzene-1,4-diamine C16 H18 N6 S WGPQOBMGPFXDSX-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
18K	BindingDB:  3SW4	Ki: 700 (nM) from 1 assay(s)
		Kd: min: 190, max: 4791 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.208 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.477	α = 90
b = 72.144	β = 90
c = 72.342	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
MD2	data collection
HKL-2000	data reduction
HKL-2000	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-01 
Deposition Author(s): Kang, Y.N., Stuckey, J.A.

Revision History  

• Version 1.0: 2012-08-01
  Type: Initial release
  
• Version 1.1: 2013-05-29
  Changes: Other
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary