Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 36.35 kDa 
• Atom Count: 2533 
• Modelled Residue Count: 273 
• Deposited 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): Yes 


• 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.392 
• R-Value Work: 0.320 
• R-Value Observed: 0.324 

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:  
  4I5M, 4I5P, 4I6B, 4I6F, 4I6H


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PLK2	A	308	Homo sapiens	Mutation(s): 7  Gene Names: PLK2, SNK EC: 2.7.11.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYY3 (Homo sapiens) Explore Q9NYY3  Go to UniProtKB:  Q9NYY3
PHAROS:  Q9NYY3 GTEx:  ENSG00000145632

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R78 (Subject of Investigation/LOI)	B [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
R78	BindingDB:  4I5M	Ki: 1 (nM) from 1 assay(s)
		Kd: 0.81 (nM) from 1 assay(s)
		IC50: min: 14, max: 30 (nM) from 3 assay(s)
	PDBBind:  4I5M	IC50: 8.8 (nM) from 1 assay(s)
	Binding MOAD:  4I5M	IC50: 8.8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.392 
• R-Value Work: 0.320 
• R-Value Observed: 0.324 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.329	α = 90
b = 60.217	β = 107.4
c = 53.213	γ = 90

Software Package:

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

Structure Validation

Ligand Structure Quality Assessment  

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
  Changes: Structure summary