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: 28.29 kDa 
• Atom Count: 1,813 
• Modelled Residue Count: 215 
• Deposited Residue Count: 242 
• Unique protein chains: 2

 4WHH

A New Class of Peptidomimetics Targeting the Polo-box Domain of Polo-like kinase 1

• PDB DOI:  https://doi.org/10.2210/pdb4WHH/pdb

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


• Deposited: 2014-09-22 Released: 2014-12-03 
• Deposition Author(s): Bang, J.K.
• Funding Organization(s): Korea Basic Science Institute, Rural Development Administration

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.236 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Literature

A new class of peptidomimetics targeting the polo-box domain of polo-like kinase 1.

Ahn, M., Han, Y.H., Park, J.E., Kim, S., Lee, W.C., Lee, S.J., Gunasekaran, P., Cheong, C., Shin, S.Y., Kim, H.Y., Ryu, E.K., Murugan, R.N., Kim, N.H., Bang, J.K.

(2015) J Med Chem 58: 294-304

• PubMed: 25347203 
• DOI: https://doi.org/10.1021/jm501147g
• Primary Citation of Related Structures:  
  4RCP, 4WHH, 4WHK, 4WHL


• PubMed Abstract: 
  

Recent progress in the development of peptide-derived Polo-like kinase (Plk1) polo-box domain (PBD) inhibitors has led to the synthesis of multiple peptide ligands with high binding affinity and selectivity. However, few systematic analyses have been conducted to identify key Plk1 residues and characterize their interactions with potent Plk1 peptide inhibitors. We performed systematic deletion analysis using the most potent 4j peptide and studied N-terminal capping of the minimal peptide with diverse organic moieties, leading to the identification of the peptidomimetic 8 (AB-103) series with high binding affinity and selectivity. To evaluate the bioavailability of short peptidomimetic ligands, PEGylated 8 series were synthesized and incubated with HeLa cells to test for cellular uptake, antiproliferative activity, and Plk1 kinase inhibition. Finally, crystallographic studies of the Plk1 PBD in complex with peptidomimetics 8 and 22 (AB-103-5) revealed the presence of two hydrogen bond interactions responsible for their high binding affinity and selectivity.

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Organizational Affiliation: 

Division of Magnetic Resonance, Korea Basic Science Institute , 804-1, Yangcheong Ri, Ochang, Chungbuk, Cheongwon 363-883, Republic of Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PLK1	A	237	Homo sapiens	Mutation(s): 0  Gene Names: PLK1, PLK 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
C6H5(CH2)8-DERIVATIZED PEPTIDE INHIBITOR	B	5	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
56A	B	L-PEPTIDE LINKING	C20 H29 N3 O2		HIS
TPO	B	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_002127	B	C6H5(CH2)8-derivatized peptide inhibitor	Polypeptide / Enzyme inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.236 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.927	α = 90
b = 58.3	β = 90
c = 66.753	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
ADSC	data collection
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-12-03 
Deposition Author(s): Bang, J.K.

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Funding Organization	Location	Grant Number
Korea Basic Science Institute	Korea, Republic Of	T34418
Rural Development Administration	Korea, Republic Of	PJ009594

Revision History  

• Version 1.0: 2014-12-03
  Type: Initial release
  
• Version 1.1: 2015-01-21
  Changes: Database references
• Version 2.0: 2019-03-27
  Changes: Data collection, Database references, Derived calculations, Other, Polymer sequence, Source and taxonomy