Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
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: 36353.84 
• Atom Count: 2265 
• Residue Count: 308 
• Unique protein chains: 1

4I5M

Selective & Brain-Permeable Polo-like Kinase-2 (Plk-2) Inhibitors that Reduce -Synuclein Phosphorylation in Rat Brain

• DOI: 10.2210/pdb4I5M/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 7 


• Deposited: 2012-11-28 Released: 2013-12-25 
• Deposition Author(s): Aubele, D.L., Hom, R.K., Adler, M., Galemmo Jr., R.A., Bowers, S., Truong, A.P., Pan, H., Beroza, P., Neitz, R.J., Yao, N., Lin, M., Tonn, G., Zhang, H., Bova, M.P., Ren, Z., Tam, D., Ruslim, L., Baker, J., Diep, L., Fitzgerald, K., Hoffman, J., Motter, R., Fauss, D., Tanaka, P., Dappen, M., Jagodzinski, J., Chan, W., Konradi, A.W., Latimer, L., Zhu, Y.L., Artis, D.R., Sham, H.L., Anderson, J.P., Bergeron, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.801 Å
• R-Value Free: 0.392 
• R-Value Work: 0.320 

Literature

Selective and brain-permeable polo-like kinase-2 (Plk-2) inhibitors that reduce alpha-synuclein phosphorylation in rat brain.

Aubele, D.L., Hom, R.K., Adler, M., Galemmo, R.A., Bowers, S., Truong, A.P., Pan, H., Beroza, P., Neitz, R.J., Yao, N., Lin, M., Tonn, G., Zhang, H., Bova, M.P., Ren, Z., Tam, D., Ruslim, L., Baker, J., Diep, L., Fitzgerald, K., Hoffman, J., Motter, R., Fauss, D., Tanaka, P., Dappen, M., Jagodzinski, J., Chan, W., Konradi, A.W., Latimer, L., Zhu, Y.L., Sham, H.L., Anderson, J.P., Bergeron, M., Artis, D.R.

(2013) Chemmedchem 8: 1295-1313

• PubMed: 23794260 
• DOI: 10.1002/cmdc.201300166
• Primary Citation of Related Structures:  
  4I6H, 4I6F, 4I6B, 4I5P


• PubMed Abstract: 
  

Polo-like kinase-2 (Plk-2) has been implicated as the dominant kinase involved in the phosphorylation of α-synuclein in Lewy bodies, which are one of the hallmarks of Parkinson's disease neuropathology. Potent, selective, brain-penetrant inhibitors of Plk-2 were obtained from a structure-guided drug discovery approach driven by the first reported Plk-2-inhibitor complexes. The best of these compounds showed excellent isoform and kinome-wide selectivity, with physicochemical properties sufficient to interrogate the role of Plk-2 inhibition in vivo. One such compound significantly decreased phosphorylation of α-synuclein in rat brain upon oral administration and represents a useful probe for future studies of this therapeutic avenue toward the potential treatment of Parkinson's disease.

---

Organizational Affiliation: 

Molecular Discovery, Elan Pharmaceuticals, 180 Oyster Point Boulevard, South San Francisco, CA 94080, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Serine/threonine-protein kinase PLK2	A	308	Homo sapiens	Mutation(s): 7  Gene Names: PLK2 (SNK) EC: 2.7.11.21
Find proteins for Q9NYY3 (Homo sapiens) Go to Gene View: PLK2 Go to UniProtKB:  Q9NYY3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
R78	A	4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide C28 H39 N7 O3 XQVVPGYIWAGRNI-JOCHJYFZSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
R78	IC50: 16.8 - 30 nM (97) BINDINGDB
R78	Kd: 0.8 nM (97) BINDINGDB
R78	Ki: <1 nM (97) BINDINGDB
R78	IC50: 8.8 nM BINDINGMOAD
R78	IC50: 8.8 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.801 Å
• R-Value Free: 0.392 
• R-Value Work: 0.320 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 104.329	α = 90.00
b = 60.217	β = 107.40
c = 53.213	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
REFMAC	refinement
AMoRE	phasing
HKL-2000	data scaling
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-11-28 
• Released Date: 2013-12-25 
• Deposition Author(s): Aubele, D.L., Hom, R.K., Adler, M., Galemmo Jr., R.A., Bowers, S., Truong, A.P., Pan, H., Beroza, P., Neitz, R.J., Yao, N., Lin, M., Tonn, G., Zhang, H., Bova, M.P., Ren, Z., Tam, D., Ruslim, L., Baker, J., Diep, L., Fitzgerald, K., Hoffman, J., Motter, R., Fauss, D., Tanaka, P., Dappen, M., Jagodzinski, J., Chan, W., Konradi, A.W., Latimer, L., Zhu, Y.L., Artis, D.R., Sham, H.L., Anderson, J.P., Bergeron, M.

Revision History 

• Version 1.0: 2013-12-25
  Type: Initial release
• Version 1.1: 2014-10-08
  Type: Structure summary