9R1Y | pdb_00009r1y

PLK1 SURFACE ENTROPY REDUCTION (SER) MUTANT IN COMPLEX WITH INHIBITOR GSK461364

PDB DOI: https://doi.org/10.2210/pdb9R1Y/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2025-04-28 Released: 2025-11-26
Deposition Author(s): Hillig, R.C., Schulze, V.K., Siemeister, G., Schmitz, A.A., Eberspaecher, U.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.218 (Depositor), 0.215 (DCC)
R-Value Work:
0.185 (Depositor), 0.188 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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 Biol Crystallogr 81

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

Macromolecule Content

Total Structure Weight: 75.44 kDa
Atom Count: 5,010
Modeled Residue Count: 585
Deposited Residue Count: 650
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PLK1	A [auth AAA], B [auth BBB]	325	Homo sapiens	Mutation(s): 2 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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53350
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JCQ (Subject of Investigation/LOI) Query on A1JCQ Download Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain O [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain O [auth BBB] mmCIF format, chain C [auth AAA] mmCIF format, chain O [auth BBB]	C [auth AAA], O [auth BBB]	5-[6-[(4-methylpiperazin-1-yl)methyl]benzimidazol-1-yl]-3-[(1~{R})-1-[2-(trifluoromethyl)phenyl]ethoxy]thiophene-2-carboxamide C₂₇ H₂₈ F₃ N₅ O₂ S ZHJGWYRLJUCMRT-QGZVFWFLSA-N		Interactions Focus chain C [auth AAA] Focus chain O [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain O [auth BBB]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth AAA] SDF format, chain E [auth AAA] SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain H [auth AAA] SDF format, chain I [auth AAA] SDF format, chain P [auth BBB] SDF format, chain Q [auth BBB] MOL2 format, chain D [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain P [auth BBB] MOL2 format, chain Q [auth BBB] mmCIF format, chain D [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain P [auth BBB] mmCIF format, chain Q [auth BBB]	D [auth AAA] E [auth AAA] F [auth AAA] G [auth AAA] H [auth AAA] D [auth AAA], E [auth AAA], F [auth AAA], G [auth AAA], H [auth AAA], I [auth AAA], P [auth BBB], Q [auth BBB]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain P [auth BBB] Focus chain Q [auth BBB] Interactions & Density Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain P [auth BBB] Focus chain Q [auth BBB]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth AAA] SDF format, chain L [auth AAA] SDF format, chain M [auth AAA] SDF format, chain N [auth AAA] SDF format, chain R [auth BBB] MOL2 format, chain K [auth AAA] MOL2 format, chain L [auth AAA] MOL2 format, chain M [auth AAA] MOL2 format, chain N [auth AAA] MOL2 format, chain R [auth BBB] mmCIF format, chain K [auth AAA] mmCIF format, chain L [auth AAA] mmCIF format, chain M [auth AAA] mmCIF format, chain N [auth AAA] mmCIF format, chain R [auth BBB]	K [auth AAA], L [auth AAA], M [auth AAA], N [auth AAA], R [auth BBB]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain M [auth AAA] Focus chain N [auth AAA] Focus chain R [auth BBB] Interactions & Density Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain M [auth AAA] Focus chain N [auth AAA] Focus chain R [auth BBB]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth AAA] MOL2 format, chain J [auth AAA] mmCIF format, chain J [auth AAA]	J [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth AAA] Interactions & Density Focus chain J [auth AAA]