9R8B | pdb_00009r8b

CRYSTAL STRUCTURE OF WILD-TYPE PLK1 KINASE DOMAIN IN COMPLEX WITH THIAZOLIDINONE INHIBITOR COMPOUND 1 AND A SELECTIVE DARPIN

• PDB DOI: https://doi.org/10.2210/pdb9R8B/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2025-05-16 Released: 2025-11-26 
• Deposition Author(s): Hillig, R.C., Matias, P.M., Bandeiras, T.M., Siemeister, G., Schulze, V.K., Schmitz, A.A., Eberspaecher, U.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.238 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Polo-like kinase 1-inhibitor co-complex structures via the surface-entropy reduction approach and a DARPin-assisted approach.

Eberspaecher, U., Schmitz, A.A., Siemeister, G., Bomer, U., Bandeiras, T.M., Matias, P.M., Schulze, V.K., Hillig, R.C.

(2025) Acta Crystallogr D Struct Biol 81: 718-733

• PubMed: 41246821 
• DOI: https://doi.org/10.1107/S2059798325009325
• Primary Citation Related Structures: 
  9R1W, 9R1X, 9R1Y, 9R8B, 9R8C


• PubMed Abstract: 
  

  Polo-like kinase 1 (PLK1) is a major regulator of cell division and has been pursued as a drug target for cancer therapy for a long time. Crystallization of the kinase domain has proven to be exceptionally challenging. Previously, we published a crystallization approach using a PLK1-specific designed ankyrin-repeat protein (DARPin) as a crystallization facilitator. Here, we report an alternative route: crystallization was successful after the introduction of a double mutation which reduced surface entropy and enabled the formation of a new crystal contact. This new PLK1 crystallization system was used to determine the first co-complex crystal structure of the Bayer thiazolidinone lead series, as well as crystal structures with representatives of two competitor inhibitor series. The molecular binding modes of these three inhibitors are analysed and discussed, and the surface-entropy reduction approach is compared with the surface modifications employed by us and others to enable the crystallization of PLK1.

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Organizational Affiliation: 
• Research and Development, Pharmaceuticals, Bayer AG, Muellerstrasse 178, 13353 Berlin, Germany.
Nuvisan ICB GmbH, Muellerstrasse 178, 13353 Berlin, Germany.
iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal.

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 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: 108.88 kDa 
• Atom Count: 7,196 
• Modeled Residue Count: 843 
• Deposited Residue Count: 964 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PLK1	A, B	315	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
DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN), variant 3H10	C, D	167	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1JCP	E [auth A], H [auth B]	(2~{Z})-2-cyano-2-[3-ethyl-5-[(~{E})-[2-[methyl-(1-methylpiperidin-4-yl)amino]pyridin-4-yl]iminomethyl]-4-oxidanylidene-1,3-thiazol-2-ylidene]-~{N}-[2,2,2-tris(fluoranyl)ethyl]ethanamide C23 H28 F3 N7 O2 S GTQIHYRIVZRZQE-DLTYULCUSA-N
GOL	F [auth A], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.238 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.072	α = 90
b = 136.899	β = 90
c = 140.729	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PHASER	phasing
SCALA	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Hillig, R.C., Matias, P.M., Bandeiras, T.M., Siemeister, G., Schulze, V.K., Schmitz, A.A., Eberspaecher, U.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release
  
• Version 1.1: 2025-12-10
  Changes: Database references