9r8b

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

Method: X-RAY DIFFRACTION Dmax: 96.3 Å Quality: EXCELLENT

1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine/threonine-protein kinase PLK1

Homo sapiens

UniProt P53350

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 33–345 Not recorded DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN), variant 3H10 × 1 A1JCP (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 × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;303 K;0.1 M TRIS-HCL PH 8.0, 8% PEG 5000 MME, 0.01 M EDTA SODIUM SALT AT 303 K. Resolution 2.20 Å R-free 0.238
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 33–345 Not recorded DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN), variant 3H10 × 1 A1JCP (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 × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;303 K;0.1 M TRIS-HCL PH 8.0, 8% PEG 5000 MME, 0.01 M EDTA SODIUM SALT AT 303 K. Resolution 2.20 Å R-free 0.238

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

84 other PDB entries and 111 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PLK1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–315; UniProt 33–345 Author chain B; PDBConstruct 3–315; UniProt 33–345

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9r8b

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9r8b
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9r8b
Deposition date deposition_date2025-05-16
Structure title titleCRYSTAL STRUCTURE OF WILD-TYPE PLK1 KINASE DOMAIN IN COMPLEX WITH THIAZOLIDINONE INHIBITOR COMPOUND 1 AND A SELECTIVE DARPIN
Keywords keywords;DESIGN ANKYRIN REPEAT PROTEIN, DARPIN, SMALL MOLECULE INHIBITOR, DRUG DESIGN, KINASE, SERINE/THREONINE-PROTEIN KINASE, KINASE DOMAIN, TRANSFERASE ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier30.81
Radius of gyration Rg (electron density) rg_electron30.07
Forward intensity I(0) i0275345000.00
Molecular weight molecular_weight88739.0 kDa
Excluded volume excluded_volume85915 ų
Envelope volume envelope_volume152730 ų
Hydration-shell volume shell_volume41178 ų
Envelope diameter envelope_diameter101.0
Shell Rg shell_rg38.13
Envelope Rg envelope_rg30.26
Shape Rg shape_rg30.07
Total Rg total_rg30.59
Total atoms total_atoms6735
Residues n_residues843
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax96.3
Rg (real space) rg_real30.65
Rg uncertainty (real space) rg_real_error0.59
I(0) (real space) i0_real2.7530e+08
I(0) uncertainty (real space) i0_real_error3.9520e+06
Rg (reciprocal space) rg_reciprocal30.72
I(0) (reciprocal space) i0_reciprocal275400000.0000
Solution quality estimate total_estimate0.9033
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.5
Skewness Skewness skewness0.146
Kurtosis Kurtosis kurtosis-0.489
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha39530000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.952

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (2)

9. Files and Curves (10)