9R8C | pdb_00009r8c

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/pdb9R8C/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda ascovirus 1a, 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., Schulze, V.K., Siemeister, G., Schmitz, A.A., Eberspaecher, U., Bomer, U.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 
  0.236 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.193 (DCC) 

Starting Model: experimental

Literature

PLK1-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 Biol Crystallogr 81

• DOI: https://doi.org/10.1107/S2059798325009325

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 109.03 kDa 
• Atom Count: 7,107 
• Modeled Residue Count: 839 
• 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 3H10	C, D	167	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R78 (Subject of Investigation/LOI)	E [auth A], H [auth B]	4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide C28 H39 N7 O3 XQVVPGYIWAGRNI-JOCHJYFZSA-N
GOL	F [auth A], G [auth A], I [auth B], J [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free:  0.236 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.193 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.605	α = 90
b = 135.302	β = 90
c = 136.7	γ = 90

Software Package:

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

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., Schulze, V.K., Siemeister, G., Schmitz, A.A., Eberspaecher, U., Bomer, U.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release