2B53 | pdb_00002b53

Human cyclin dependent kinase 2 (CDK2) complexed with DIN-234325

• PDB DOI: https://doi.org/10.2210/pdb2B53/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2005-09-27 Released: 2005-10-11 
• Deposition Author(s): Muckelbauer, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.273 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.230 (DCC) 

Literature

Quinazolines as Cyclin Dependent Kinase Inhibitors

Sielecki, T.M., Johnson, T.L., Liu, J., Muckelbauer, J.K., Grafstrom, R.H., Cox, S., Boylan, J., Burton, C.R., Chen, H., Smallwood, A., Chang, C.-H., Boisclair, M., Benfield, P.A., Trainor, G.L., Seitz, S.P.

(2001) Bioorg Med Chem Lett 11: 1157-1160

• PubMed: 11354366 
• DOI: https://doi.org/10.1016/s0960-894x(01)00185-8
• Primary Citation Related Structures: 
  2B53


• PubMed Abstract: 
  

  Quinazolines have been identified as inhibitors of CDK4/D1 and CDK2/E. Aspects of the SAR were investigated using solution-phase, parallel synthesis. An X-ray crystal structure was obtained of quinazoline 51 bound in CDK2 and key interactions within the ATP binding pocket are defined.

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Organizational Affiliation: 
• The DuPont Pharmaceuticals Company, Wilmington, DE 19880-0500, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.34 kDa 
• Atom Count: 2,465 
• Modeled Residue Count: 294 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein kinase 2	A	298	Homo sapiens	Mutation(s): 0  EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (UniProt)
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
D23	B [auth A]	6-(3-AMINOPHENYL)-N-(TERT-BUTYL)-2-(TRIFLUOROMETHYL)QUINAZOLIN-4-AMINE C19 H19 F3 N4 XQKJVNGGVLHNLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.273 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.230 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.96	α = 90
b = 73.51	β = 90
c = 54.28	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
CNX	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-11 
Deposition Author(s): Muckelbauer, J.

Revision History  

• Version 1.0: 2005-10-11
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations