Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 27 kDa 
• Atom Count: 1,891 
• Modelled Residue Count: 222 
• Deposited Residue Count: 232 
• Unique protein chains: 2

 4HY2

Crystal structure of Plk1 Polo-box domain in complex with PL-42

• PDB DOI:  https://doi.org/10.2210/pdb4HY2/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-11-12 Released: 2013-04-03 
• Deposition Author(s): Lee, W.C., Song, J.H., Kim, H.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.246 
• R-Value Work: 0.199 

Literature

Development of cyclic peptomer inhibitors targeting the polo-box domain of polo-like kinase 1.

Murugan, R.N., Park, J.E., Lim, D., Ahn, M., Cheong, C., Kwon, T., Nam, K.Y., Choi, S.H., Kim, B.Y., Yoon, D.Y., Yaffe, M.B., Yu, D.Y., Lee, K.S., Bang, J.K.

(2013) Bioorg Med Chem 21: 2623-2634

• PubMed: 23498919 
• DOI: https://doi.org/10.1016/j.bmc.2013.02.020
• Primary Citation of Related Structures:  
  4HAB, 4HY2


• PubMed Abstract: 
  

The polo-box domain (PBD) of polo-like kinase 1 (Plk1) is essentially required for the function of Plk1 in cell proliferation. The availability of the phosphopeptide-binding pocket on PBD provides a unique opportunity to develop novel protein-protein interaction inhibitors. Recent identification of a minimal 5-residue-long phosphopeptide, PLHSpT, as a Plk1 PBD-specific ligand has led to the development of several peptide-based inhibitors, but none of them is cyclic peptide. Through the combination of single-peptoid mimics and thio-ether bridged cyclization, we successfully demonstrated for the first time two cyclic peptomers, PL-116 and PL-120, dramatically improved the binding affinity without losing mono-specificity against Plk1 PBD in comparison with the linear parental peptide, PLHSpT. These cyclic peptomers could serve as promising templates for future drug designs to inhibit Plk1 PBD.

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Organizational Affiliation: 

Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk 363-883, Cheongwon, Republic of Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PLK1	A	225	Homo sapiens	Mutation(s): 0  Gene Names: PLK, PLK1 EC: 2.7.11.21
UniProt & NIH Common Fund Data Resources
Find proteins for P53350 (Homo sapiens) Explore P53350  Go to UniProtKB:  P53350
PHAROS:  P53350

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PL-42	B [auth D]	7	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	B [auth D]	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000922	B [auth D]	PL-42	Peptide-like / Inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.246 
• R-Value Work: 0.199 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.4253	α = 90
b = 50.2621	β = 101.5152
c = 57.4562	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Lee, W.C., Song, J.H., Kim, H.Y.

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2013-05-22
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description, Source and taxonomy