Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 35.07 kDa 
• Atom Count: 2561 
• Modelled Residue Count: 294 
• Deposited Residue Count: 306 
• Unique protein chains: 1

3RJC

CDK2 in complex with inhibitor L4-12

• PDB DOI: 10.2210/pdb3RJC/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-04-15 Released: 2012-10-31 
• Deposition Author(s): Betzi, S., Alam, R., Han, H., Becker, A., Schonbrunn, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.250 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 

Literature

Development of highly potent and selective diaminothiazole inhibitors of cyclin-dependent kinases.

Schonbrunn, E., Betzi, S., Alam, R., Martin, M.P., Becker, A., Han, H., Francis, R., Chakrasali, R., Jakkaraj, S., Kazi, A., Sebti, S.M., Cubitt, C.L., Gebhard, A.W., Hazlehurst, L.A., Tash, J.S., Georg, G.I.

(2013) J Med Chem 56: 3768-3782

• PubMed: 23600925 
• DOI: 10.1021/jm301234k
• Primary Citation of Related Structures:  
  3QQK, 3QTQ, 3QTR, 3QTS, 3QTU, 3QTW, 3QTX, 3QTZ, 3QU0, 3QXP, 3R8U, 3R8V, 3R8Z, 3R9D, 3R9H, 3R9N, 3R9O, 3RAH, 3RAK, 3RAL, 3RJC, 3RK5, 3RK7, 3RK9, 3RKB, 3RMF, 3RNI, 3RPR, 3RPV, 3RPY, 3RZB, 3S00, 3S0O, 3S1H, 3SQQ, 4GCJ


• PubMed Abstract: 
  

Cyclin-dependent kinases (CDKs) are serine/threonine protein kinases that act as key regulatory elements in cell cycle progression. We describe the development of highly potent diaminothiazole inhibitors of CDK2 (IC50 = 0.0009-0.0015 μM) from a single hit compound with weak inhibitory activity (IC50 = 15 μM), discovered by high-throughput screening. Structure-based design was performed using 35 cocrystal structures of CDK2 liganded with distinct analogues of the parent compound. The profiling of compound 51 against a panel of 339 kinases revealed high selectivity for CDKs, with preference for CDK2 and CDK5 over CDK9, CDK1, CDK4, and CDK6. Compound 51 inhibited the proliferation of 13 out of 15 cancer cell lines with IC50 values between 0.27 and 6.9 μM, which correlated with the complete suppression of retinoblastoma phosphorylation and the onset of apoptosis. Combined, the results demonstrate the potential of this new inhibitors series for further development into CDK-specific chemical probes or therapeutics.

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Organizational Affiliation: 

Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	A	306	Homo sapiens	Mutation(s): 0  Gene Names: CDK2, CDKN2 EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens) Explore P24941  Go to UniProtKB:  P24941
PHAROS:  P24941

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
06Z	B [auth A]	{4-amino-2-[(3-fluorophenyl)amino]-1,3-thiazol-5-yl}(phenyl)methanone C16 H12 F N3 O S CGDCHWZCEONCMK-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
06Z	PDBBind:  3RJC	IC50: 5700 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.250 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.38	α = 90
b = 71.55	β = 90
c = 71.7	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
CNS	refinement
XDS	data reduction
XDS	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-04-15 
• Released Date: 2012-10-31 
Deposition Author(s): Betzi, S., Alam, R., Han, H., Becker, A., Schonbrunn, E.

Revision History  

• Version 1.0: 2012-10-31
  Type: Initial release
  
• Version 1.1: 2013-05-15
  Changes: Database references
• Version 1.2: 2013-06-05
  Changes: Database references