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- PDB-9r1x: PLK1 SURFACE ENTROPY REDUCTION (SER) MUTANT IN COMPLEX WITH INHIB... -

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Basic information

Entry
Database: PDB / ID: 9r1x
TitlePLK1 SURFACE ENTROPY REDUCTION (SER) MUTANT IN COMPLEX WITH INHIBITOR BI 2536
ComponentsSerine/threonine-protein kinase PLK1
KeywordsTRANSFERASE / SURFACE ENTROPY REDUCTION / SER / SMALL MOLECULE INHIBITOR / DRUG DESIGN / KINASE / SERINE/THREONINE-PROTEIN KINASE
Function / homology
Function and homology information


Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / polo kinase / mitotic nuclear membrane disassembly / protein localization to nuclear envelope / Phosphorylation of Emi1 / homologous chromosome segregation ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / polo kinase / mitotic nuclear membrane disassembly / protein localization to nuclear envelope / Phosphorylation of Emi1 / homologous chromosome segregation / metaphase/anaphase transition of mitotic cell cycle / female meiosis chromosome segregation / nuclear membrane disassembly / synaptonemal complex / Phosphorylation of the APC/C / anaphase-promoting complex binding / Golgi inheritance / outer kinetochore / positive regulation of ubiquitin protein ligase activity / microtubule bundle formation / double-strand break repair via alternative nonhomologous end joining / mitotic chromosome condensation / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / regulation of mitotic spindle assembly / centrosome cycle / regulation of mitotic metaphase/anaphase transition / sister chromatid cohesion / positive regulation of ubiquitin-protein transferase activity / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / spindle midzone / mitotic G2 DNA damage checkpoint signaling / regulation of anaphase-promoting complex-dependent catabolic process / mitotic cytokinesis / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / positive regulation of proteolysis / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / negative regulation of double-strand break repair via homologous recombination / Cyclin A/B1/B2 associated events during G2/M transition / protein localization to chromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / centriole / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Mitotic Prometaphase / Anchoring of the basal body to the plasma membrane / EML4 and NUDC in mitotic spindle formation / regulation of mitotic cell cycle / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / Condensation of Prophase Chromosomes / mitotic spindle organization / regulation of cytokinesis / establishment of protein localization / RHO GTPases Activate Formins / peptidyl-serine phosphorylation / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / protein destabilization / kinetochore / positive regulation of protein localization to nucleus / G2/M transition of mitotic cell cycle / centriolar satellite / spindle / spindle pole / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / double-strand break repair / microtubule cytoskeleton / midbody / microtubule binding / protein phosphorylation / protein kinase activity / regulation of cell cycle / protein ubiquitination / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / protein kinase binding / negative regulation of apoptotic process / chromatin / magnesium ion binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-R78 / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsHillig, R.C. / Schulze, V.K. / Siemeister, G. / Schmitz, A.A. / Eberspaecher, U.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2025
Title: Polo-like kinase 1-inhibitor co-complex structures via the surface-entropy reduction approach and a DARPin-assisted approach.
Authors: Eberspaecher, U. / Schmitz, A.A. / Siemeister, G. / Bomer, U. / Bandeiras, T.M. / Matias, P.M. / Schulze, V.K. / Hillig, R.C.
History
DepositionApr 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK1
B: Serine/threonine-protein kinase PLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,90112
Polymers73,0932
Non-polymers1,80810
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-87 kcal/mol
Surface area28530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.515, 104.497, 71.329
Angle α, β, γ (deg.)90.00, 115.63, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-524-

HOH

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Components

#1: Protein Serine/threonine-protein kinase PLK1 / Polo-like kinase 1 / PLK-1 / Serine/threonine-protein kinase 13 / STPK13


Mass: 36546.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL GLY-SER ARE CLONING ARTIFACT FROM THROMBIN CLEAVAGE SITE. DOUBLE SURFACE ENTROPY REDUCTION (SER) MUTATION K225D/K226A DESIGNED TO INCREASE THE LIKELIHOOD OF CRYSTALLIZATION SUCCESS.
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53350, polo kinase
#2: Chemical ChemComp-R78 / 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


Mass: 521.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H39N7O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: sodium acetate, ammonium sulphate, MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.84→42.1 Å / Num. obs: 16036 / % possible obs: 91.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 33.3 Å2 / Rsym value: 0.12 / Net I/σ(I): 10.4
Reflection shellResolution: 2.84→2.93 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1488 / Rsym value: 0.41 / % possible all: 53.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALEPACKdata scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→42.1 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.856 / SU B: 42.54 / SU ML: 0.41 / Cross valid method: THROUGHOUT / ESU R Free: 0.473 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27746 817 5.1 %RANDOM
Rwork0.21875 ---
obs0.22166 15216 91.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.24 Å2
Baniso -1Baniso -2Baniso -3
1-4.41 Å20 Å22.29 Å2
2---1.03 Å20 Å2
3----3.82 Å2
Refinement stepCycle: 1 / Resolution: 2.84→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4723 0 117 64 4904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0135038
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154868
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.6736832
X-RAY DIFFRACTIONr_angle_other_deg1.0311.60911242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9055608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.520.325277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63315896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5721548
X-RAY DIFFRACTIONr_chiral_restr0.0390.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026132
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021172
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1383.3122363
X-RAY DIFFRACTIONr_mcbond_other2.1313.3112362
X-RAY DIFFRACTIONr_mcangle_it3.6457.4462958
X-RAY DIFFRACTIONr_mcangle_other3.6467.4482959
X-RAY DIFFRACTIONr_scbond_it2.2073.6052674
X-RAY DIFFRACTIONr_scbond_other2.1983.5922671
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7267.963857
X-RAY DIFFRACTIONr_long_range_B_refined6.5339.5235336
X-RAY DIFFRACTIONr_long_range_B_other6.52839.5335334
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9324 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.842→2.916 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 28 -
Rwork0.306 580 -
obs--48.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.7972-1.6881-0.47296.8831-0.93835.32250.0720.70090.49160.32820.1590.2559-0.9287-0.3353-0.2310.22950.0807-0.05760.18310.13370.332225.38514.859-1.76
22.9712-0.15920.43940.81930.09561.3301-0.02020.229-0.2294-0.08030.01920.12490.26960.01140.0010.0749-0.0109-0.03130.0195-0.01360.423235.626-4.91712.154
33.3194-1.2042-0.54334.1749-0.46424.4010.1522-0.1233-0.10640.6908-0.178-0.59720.29321.03420.02580.21310.0365-0.2010.37660.03960.568115.343-30.5134.641
42.36221.28010.01693.01640.03371.1706-0.05250.10790.30770.0020.00040.2344-0.13720.1220.05210.0305-0.0352-0.05140.04810.03240.5292-3.686-18.82820.782
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 132
2X-RAY DIFFRACTION2A133 - 334
3X-RAY DIFFRACTION3B39 - 132
4X-RAY DIFFRACTION4B133 - 326

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