2B53

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.223 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/10.1016/s0960-894x(01)00185-8
  • Primary Citation of 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.


  • Organizational Affiliation

    The DuPont Pharmaceuticals Company, Wilmington, DE 19880-0500, USA. thais.m.sielecki@dupontpharma.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division protein kinase 2298Homo sapiensMutation(s): 0 
EC: 2.7.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
PHAROS:  P24941
GTEx:  ENSG00000123374 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24941
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D23
Query on D23

Download Ideal Coordinates CCD File 
B [auth A]6-(3-AMINOPHENYL)-N-(TERT-BUTYL)-2-(TRIFLUOROMETHYL)QUINAZOLIN-4-AMINE
C19 H19 F3 N4
XQKJVNGGVLHNLA-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
D23 Binding MOAD:  2B53 IC50: 600 (nM) from 1 assay(s)
PDBBind:  2B53 IC50: 600 (nM) from 1 assay(s)
BindingDB:  2B53 IC50: 600 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.96α = 90
b = 73.51β = 90
c = 54.28γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNXrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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