Crystal Structure of CDK2 in complex with Macrocyclic Aminopyrimidine

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.219 

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This is version 1.3 of the entry. See complete history


Macrocyclic Aminopyrimidines as Multitarget Cdk and Vegf-R Inhibitors with Potent Antiproliferative Activities.

Luecking, U.Siemeister, G.Schaefer, M.Briem, H.Krueger, M.Lienau, P.Jautelat, R.

(2007) ChemMedChem 2: 63

  • DOI: https://doi.org/10.1002/cmdc.200600199
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    X-ray structures from CDK2-aminopyrimidine inhibitor complexes led to the idea to stabilize the active conformation of aminopyrimidine inhibitors by incorporating the recognition site into a macrocyclic framework. A modular synthesis approach that relies on a new late-stage macrocyclization protocol that enables fast and efficient synthesis of macrocyclic aminopyrimidines was developed. A set of structurally diverse derivatives was prepared. Macrocyclic aminopyrimidines were shown to be multitarget inhibitors of CDK1/2 and VEGF-RTKs. In addition, potent antiproliferative activities toward various human tumor cells and a human tumor xenograft model were demonstrated.

  • Organizational Affiliation

    Medicinal Chemistry, Research Center Europe, Schering AG, 13342 Berlin, Germany. ulrich.luecking@schering.de

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CELL DIVISION PROTEIN KINASE 2298Homo sapiensMutation(s): 0 
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PY8

Download Ideal Coordinates CCD File 
B [auth A]6-BROMO-13-THIA-2,4,8,12,19-PENTAAZATRICYCLO[,7~]NONADECA-1(18),3(19),4,6,14,16-HEXAENE 13,13-DIOXIDE
C13 H14 Br N5 O2 S
Binding Affinity Annotations 
IDSourceBinding Affinity
PY8 BindingDB:  2J9M IC50: 140 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.936α = 90
b = 69.934β = 90
c = 71.687γ = 90
Software Package:
Software NamePurpose
SAINTdata reduction
SADABSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description