7MSO | pdb_00007mso

Crystal Structure of Polo Box Domain in Complex with Cyclic Peptide Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb7MSO/pdb

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


• Deposited: 2021-05-11 Released: 2022-03-02 
• Deposition Author(s): Lim, D.C., Yaffe, M.B.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.210 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Novel Macrocyclic Peptidomimetics Targeting the Polo-Box Domain of Polo-Like Kinase 1.

Ryu, S., Park, J.E., Ham, Y.J., Lim, D.C., Kwiatkowski, N.P., Kim, D.H., Bhunia, D., Kim, N.D., Yaffe, M.B., Son, W., Kim, N., Choi, T.I., Swain, P., Kim, C.H., Lee, J.Y., Gray, N.S., Lee, K.S., Sim, T.

(2022) J Med Chem 65: 1915-1932

• PubMed: 35029981 
• DOI: https://doi.org/10.1021/acs.jmedchem.1c01359
• Primary Citation Related Structures: 
  7MSO


• PubMed Abstract: 
  

  The polo-box domain (PBD) of Plk1 is a promising target for cancer therapeutics. We designed and synthesized novel phosphorylated macrocyclic peptidomimetics targeting PBD based on acyclic phosphopeptide PMQSpTPL. The inhibitory activities of 16e on Plk1-PBD is >30-fold higher than those of PMQSpTPL. Both 16a and 16e possess excellent selectivity for Plk1-PBD over Plk2/3-PBD. Analysis of the cocrystal structure of Plk1-PBD in complex with 16a reveals that the 3-(trifluoromethyl)benzoyl group in 16a interacts with Arg516 through a π-stacking interaction. This π-stacking interaction, which has not been reported previously, provides insight into the design of novel and potent Plk1-PBD inhibitors. Furthermore, 16h , a PEGlyated macrocyclic phosphopeptide derivative, induces Plk1 delocalization and mitotic failure in HeLa cells. Also, the number of phospho-H3-positive cells in a zebrafish embryo increases in proportion to the amount of 16a . Collectively, the novel macrocyclic peptidomimetics should serve as valuable templates for the design of potent and novel Plk1-PBD inhibitors.

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Organizational Affiliation: 
• KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.
Chemical Kinomics Research Center, Korea Institute of Science and Technology, 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea.
Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States.
Koch Institute for Integrative Cancer Research, and Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02139, United States.
Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, United States.
Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States.
Department of Chemistry, College of Convergence and Integrated Science, Kyonggi University, 154 Gwanggyosan-ro, Yeongtong-gu, Suwon 16227, Republic of Korea.
Voronoibio Inc., 32 Songdogwahak-ro, Yeonsu-gu, Incheon 21984, Republic of Korea.
Divisions of Acute Care Surgery, Trauma, and Surgical Critical Care, and Surgical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, Massachusetts 02215, United States.
Department of Biology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea.
Department of Biological Sciences, Keimyung University, 1095 Dalgubeol-daero, Dalseo-gu, Daegu 42601, Republic of Korea.
Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, Stanford School of Medicine, Stanford University, 290 Jane Stanford Way, Stanford, California 94305, United States.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.28 kDa 
• Atom Count: 4,015 
• Modeled Residue Count: 447 
• Deposited Residue Count: 486 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PLK1	A, B	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 GTEx:  ENSG00000166851

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic Peptide Inhibitor ZO1-GLN-SER-TPO-45W-MLL	C [auth E], D [auth F]	6	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLL	C [auth E], D [auth F]	L-PEPTIDE LINKING	C7 H15 N O2		LEU
TPO	C [auth E], D [auth F]	L-PEPTIDE LINKING	C4 H10 N O6 P		THR
ZNY	C [auth E], D [auth F]	L-PEPTIDE LINKING	C7 H13 N O3		--

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002479	C [auth E], D [auth F]	Cyclic Peptide Inhibitor ZO1-GLN-SER-TPO-45W-MLL	Cyclic peptide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.210 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.282	α = 90
b = 64.652	β = 92.49
c = 70.163	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Lim, D.C., Yaffe, M.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	R35-ES028374

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 3.0: 2024-07-10
  Changes: Data collection, Derived calculations, Non-polymer description, Structure summary