9IM7 | pdb_00009im7

Crystal structure of mouse Plk1-PBD in complex with R12-4j compound

• PDB DOI: https://doi.org/10.2210/pdb9IM7/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-02 Released: 2025-11-05 
• Deposition Author(s): Kim, E.E., Shin, S.C.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.237 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

N-Degron-Based PROTAC Targeting PLK1: A Potential Therapeutic Strategy for Cervical Cancer.

Gunasekaran, P., Shin, S.C., Hwang, Y.S., Lee, J., La, Y.K., Yim, M.S., Kim, H.N., Kim, T.W., Yang, E., Lee, S.J., Yoon, J.M., Kim, E.E., Jeon, S., Ryu, E.K., Bang, J.K.

(2025) Pharmaceutics 17

• PubMed: 40871048 
• DOI: https://doi.org/10.3390/pharmaceutics17081027
• Primary Citation Related Structures: 
  9IM7


• PubMed Abstract: 
  

  Background : Cervical cancer remains a major global health concern, with existing chemotherapy facing limited effectiveness owing to resistance. Polo-like kinase 1 (PLK1) overexpression in cervical cancer cells is a promising target for developing novel therapies to overcome chemoresistance and improve treatment efficacy. Methods : In this study, we developed a novel PROTAC, NC1, targeting PLK1 PBD via the N-end rule pathway. Results : This PROTAC effectively depleted the PLK1 protein in HeLa cells by inducing protein degradation. The crystal structure of the PBD-NC1 complex identified key PLK1 PBD binding interactions and isothermal titration calorimetry (ITC) confirmed a binding affinity of 6.06 µM between NC1 and PLK1 PBD. NC1 significantly decreased cell viability with an IC ₅₀ of 5.23 µM, induced G2/M phase arrest, and triggered apoptosis in HeLa cells. In vivo, NC1 suppressed tumor growth in a HeLa xenograft mouse model. Conclusions : This research highlights the potential of N-degron-based PROTACs targeting the PLK1 protein in cancer therapies, highlighting their potential in future cervical anticancer treatment strategies.

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Organizational Affiliation: 
• Division of Magnetic Resonance, Korea Basic Science Institute (KBSI), Ochang, Cheongju 28119, Republic of Korea.
Dandicure Inc., Ochang, Cheongju 28119, Republic of Korea.
Convergent Research Support Division, Technological Convergence Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.
College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea.
Korea Disease Control and Prevention Agency, National Institute of Health Center for Emerging Virus Research, Division of Emerging Virus and Vector Research, Cheongju 28159, Republic of Korea.
Future Innovation Medical Research Center, Soonchunhyang University Cheonan Hospital, Cheonan 31151, Republic of Korea.
Department of Obstetrics and Gynecology, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan 31151, Republic of Korea.
Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.82 kDa 
• Atom Count: 1,904 
• Modeled Residue Count: 225 
• Deposited Residue Count: 231 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PLK1	A	224	Mus musculus	Mutation(s): 0  Gene Names: Plk1, Plk EC: 2.7.11.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q07832 (Mus musculus) Explore Q07832  Go to UniProtKB:  Q07832
IMPC:  MGI:97621

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
(ACE)(A1L2U)L(56A)S(YTH)(NH2)	B	7	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  2 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
YTH	B	THR	Phosphorylation	C4 H10 N O6 P
YTH	B	THR	Stereoisomerisation	C4 H10 N O6 P

Non-standard Monomers  2 Unique
ID	Chains	Type	Formula	2D Diagram
56A	B	L-PEPTIDE LINKING	C20 H29 N3 O2
A1L2U	B	L-PEPTIDE LINKING	C11 H20 N2 O3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.237 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.672	α = 90
b = 51.454	β = 100.9
c = 57.414	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Kim, E.E., Shin, S.C.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release