Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 34360.74 
• Atom Count: 2274 
• Residue Count: 298 
• Unique protein chains: 1

2J9M

Crystal Structure of CDK2 in complex with Macrocyclic Aminopyrimidine

• DOI: 10.2210/pdb2J9M/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• 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: 2.5 Å
• R-Value Free: 0.294 
• R-Value Work: 0.210 

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: 10.1002/cmdc.200600199


• 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]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CELL DIVISION PROTEIN KINASE 2	A	298	Homo sapiens	Mutation(s): 0  Gene Names: CDK2 (CDKN2) EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens) Go to Gene View: CDK2 Go to UniProtKB:  P24941

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PY8	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 1(5)-BROMO-4-THIA-2,5,9-TRIAZA-1(2,4)-PYRIMIDINA-3(1,3)-BENZENACYLCLANONAPHANE-4,4-DIOXIDE C13 H14 Br N5 O2 S AWSQADBSXFTFKL-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
PY8	IC50: 140 nM (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.294 
• R-Value Work: 0.210 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 52.936	α = 90.00
b = 69.934	β = 90.00
c = 71.687	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-11-13 
• 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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance