Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 34357.02 
• Atom Count: 2141 
• Residue Count: 298 
• Unique protein chains: 1

5D1J

CRYSTAL STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 (CDK2-WT) COMPLEX WITH N-[5-[[[5-(1,1-DIMETHYLETHYL)-2-OXAZOLYL] METHYL]THIO]-2-THIAZOLYL]-4-PIPERIDINECARBOXAMIDE (BMS-387032)

• DOI: 10.2210/pdb5D1J/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21


• Deposited: 2015-08-04 Released: 2015-08-12 
• Deposition Author(s): Sack, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.232 
• R-Value Work: 0.201 

Literature

N-(Cycloalkylamino)Acyl-2-Aminothiazole Inhibitors Of Cyclin-Dependent Kinase 2. N-[5-[[[5-(1,1-Dimethylethyl) -2-Oxazolyl]Methyl]Thio]-2-Thiazolyl]-4-Piperidinecarboxamide (Bms-387032), A Highly Efficacious And Selective Antitumor Agent

Misra, R.N., Xiao, H.Y., Kim, K.S., Lu, S., Han, W.C., Barbosa, S.A., Hunt, J.T., Rawlins, D.B., Shan, W., Ahmed, S.Z., Qian, L., Chen, B.C., Zhao, R., Bednarz, M.S., Kellar, K.A., Mulheron, J.G., Batorsky, R., Roongta, U., Kamath, A., Marathe, P., Ranadive, S.A., Sack, J.S., Tokarski, J.S., Pavletich, N.P., Lee, F.Y.F., Webster, K.R., Kimball, S.D.

(2004) J.Med.Chem. 47: 1719

• PubMed: 15027863 
• DOI: 10.1021/jm0305568


• PubMed Abstract: 
  

N-Acyl-2-aminothiazoles with nonaromatic acyl side chains containing a basic amine were found to be potent, selective inhibitors of CDK2/cycE which exhibit antitumor activity in mice. In particular, compound 21 [N-[5-[[[5-(1,1-dimethylethyl)-2-oxazolyl]methyl]thio]-2-thiazolyl]-4-piperidinecarboxamide, BMS-387032], has been identified as an ATP-competitive and CDK2-selective inhibitor which has been selected to enter Phase 1 human clinical trials as an antitumor agent. In a cell-free enzyme assay, 21 showed a CDK2/cycE IC(50) = 48 nM and was 10- and 20-fold selective over CDK1/cycB and CDK4/cycD, respectively. It was also highly selective over a panel of 12 unrelated kinases. Antiproliferative activity was established in an A2780 cellular cytotoxicity assay in which 21 showed an IC(50) = 95 nM. Metabolism and pharmacokinetic studies showed that 21 exhibited a plasma half-life of 5-7 h in three species and moderately low protein binding in both mouse (69%) and human (63%) serum. Dosed orally to mouse, rat, and dog, 21 showed 100%, 31%, and 28% bioavailability, respectively. As an antitumor agent in mice, 21 administered at its maximum-tolerated dose exhibited a clearly superior efficacy profile when compared to flavopiridol in both an ip/ip P388 murine tumor model and in a s.c./i.p. A2780 human ovarian carcinoma xenograft model.

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Organizational Affiliation: 

Bristol-Myers Squibb Pharmaceutical Research Institute, PO Box 4000, Princeton, New Jersey 08543-4000, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cyclin-dependent 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
56H	A	N-(5-{[(5-tert-butyl-1,3-oxazol-2-yl)methyl]sulfanyl}-1,3-thiazol-2-yl)piperidine-4-carboxamide C17 H24 N4 O2 S2 OUSFTKFNBAZUKL-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
56H	Ki: 38 nM (100) BINDINGDB
56H	Kd: 69 - 69000 nM (100) BINDINGDB
56H	IC50: 38 - 46 nM (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.232 
• R-Value Work: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 53.724	α = 90.00
b = 72.778	β = 90.00
c = 72.535	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
AMoRE	phasing
SCALEPACK	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-08-04 
• Released Date: 2015-08-12 
• Deposition Author(s): Sack, J.S.

Revision History 

• Version 1.0: 2015-08-12
  Type: Initial release
• Version 1.1: 2017-11-22
  Type: Derived calculations, Refinement description