2J9M

Crystal Structure of CDK2 in complex with Macrocyclic Aminopyrimidine

• PDB DOI: https://doi.org/10.2210/pdb2J9M/pdb

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


• Deposited: 2006-11-13 Released: 2007-11-06 
• Deposition Author(s): Schaefer, M., Luecking, U., Siemeister, G., Briem, H., Krueger, M., Lienau, P., Jautelat, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.294 
• R-Value Work: 0.210 
• R-Value Observed: 0.219 

Starting Model: experimental

Literature

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

• PubMed: 17131463 
• DOI: https://doi.org/10.1002/cmdc.200600199
• Primary Citation of Related Structures:  
  2J9M


• 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.

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Organizational Affiliation: 

Medicinal Chemistry, Research Center Europe, Schering AG, 13342 Berlin, Germany. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 34.36 kDa 
• Atom Count: 2,290 
• Modelled Residue Count: 275 
• 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
PY8	B [auth A]	6-BROMO-13-THIA-2,4,8,12,19-PENTAAZATRICYCLO[12.3.1.1~3,7~]NONADECA-1(18),3(19),4,6,14,16-HEXAENE 13,13-DIOXIDE C13 H14 Br N5 O2 S AWSQADBSXFTFKL-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PY8	BindingDB:  2J9M	IC50: 140 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 52.936	α = 90
b = 69.934	β = 90
c = 71.687	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-06 
Deposition Author(s): Schaefer, M., Luecking, U., Siemeister, G., Briem, H., Krueger, M., Lienau, P., Jautelat, R.

Revision History  

• 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