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- PDB-9o63: Crystal structure of PLK4 and RP1664 complex -

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Basic information

Entry
Database: PDB / ID: 9o63
TitleCrystal structure of PLK4 and RP1664 complex
ComponentsSerine/threonine-protein kinase PLK4
KeywordsTRANSFERASE / Kinase / Inhibitor / Cell-cycle regulated / Centrioles
Function / homology
Function and homology information


de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / procentriole / deuterosome / trophoblast giant cell differentiation / procentriole replication complex / positive regulation of centriole replication / polo kinase / XY body / centriole replication / cleavage furrow ...de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / procentriole / deuterosome / trophoblast giant cell differentiation / procentriole replication complex / positive regulation of centriole replication / polo kinase / XY body / centriole replication / cleavage furrow / cilium assembly / centriole / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleolus / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Plk4, C-terminal polo-box domain / Plk4, second cryptic polo-box domain / Plk4, first cryptic polo-box domain / Polo-like Kinase 4 Polo Box 1 / Polo-like Kinase 4 Polo Box 2 / Cryptic Polo-Box 1 (CPB1) domain profile. / Cryptic Polo-Box 2 (CPB2) domain profile. / Serine/threonine-protein kinase, first cryptic polo-box domain superfamily / : / POLO box domain ...Plk4, C-terminal polo-box domain / Plk4, second cryptic polo-box domain / Plk4, first cryptic polo-box domain / Polo-like Kinase 4 Polo Box 1 / Polo-like Kinase 4 Polo Box 2 / Cryptic Polo-Box 1 (CPB1) domain profile. / Cryptic Polo-Box 2 (CPB2) domain profile. / Serine/threonine-protein kinase, first cryptic polo-box domain superfamily / : / POLO box domain / POLO box domain profile. / Tyrosine-protein kinase, active site / Protein kinase 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
: / Serine/threonine-protein kinase PLK4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsPau, V.P.T. / Mao, D.Y.L. / Mader, P. / Maderova, Z. / Zimmermann, M. / Sicheri, F.
Funding support Canada, 3items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-178026 Canada
Canadian Institutes of Health Research (CIHR)PJT-180338 Canada
Other private
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery of RP-1664: A First-in-Class Orally Bioavailable, Selective PLK4 Inhibitor.
Authors: Vallee, F. / Casas-Selves, M. / Bubenik, M. / Duplessis, M. / Sow, B. / Suarez, C. / Sangiorgi, B. / Li, L. / Hyer, M. / Papp, R. / Leclaire, M.E. / Perryman, A.L. / Liu, B. / Surprenant, S. ...Authors: Vallee, F. / Casas-Selves, M. / Bubenik, M. / Duplessis, M. / Sow, B. / Suarez, C. / Sangiorgi, B. / Li, L. / Hyer, M. / Papp, R. / Leclaire, M.E. / Perryman, A.L. / Liu, B. / Surprenant, S. / Mochirian, P. / Pau, V. / Maderova, Z. / Mader, P. / Yin, S.Y. / Goodfellow, E. / Roulston, A. / Stocco, R. / Godbout, C. / Baruah, P. / Bonneau-Fortin, A. / Schonhoft, J.D. / Nejad, P. / Norman, D. / Truong, V.L. / Crane, S. / Attia, M.A. / Mao, D. / Sicheri, F. / Marshall, C.G. / Zimmermann, M. / Bendahan, D. / Gallant, M. / Black, W.C.
History
DepositionApr 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4304
Polymers31,7241
Non-polymers7073
Water68538
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.140, 83.890, 52.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Serine/threonine-protein kinase PLK4 / Polo-like kinase 4 / PLK-4 / Serine/threonine-protein kinase 18 / Serine/threonine-protein kinase Sak


Mass: 31723.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The missing part are disordered loop or regions in the x-ray structure
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK4, SAK, STK18 / Plasmid: pET42a(+)-GST-6HIS-TEV-SL-PLK4(2-267) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: O00444, polo kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-A1CAD / 5-cyclopropyl-N~2~-[2,6-difluoro-4-(methanesulfonyl)phenyl]-N~2~-methyl-6-(1-methyl-1H-imidazol-4-yl)-N~4~-(5-methyl-1H-pyrazol-3-yl)pyrimidine-2,4-diamine


Mass: 514.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24F2N8O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.8 % / Description: Plate Cluster
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 9 - 14% PEG4K, 0.1 M Na Cit; pH 5.4 - 5.5, 0.2 M (NH4)2SO4
PH range: 5.4 - 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.26→44.54 Å / Num. obs: 25230 / % possible obs: 99.66 % / Redundancy: 4.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.163 / Net I/σ(I): 3.87
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.26-2.41.44413410.0571.6311
2.4-2.561.40512800.1681.9511
2.56-2.760.89911770.3721.2421
2.76-3.030.46310870.740.6321
3.03-3.380.2289950.8830.3081
3.38-3.90.0958990.9770.1251
3.9-4.770.0537290.9950.071
4.77-6.710.0575560.9880.0751
6.71-44.540.0343040.9970.0441

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→44.54 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2636 680 5 %
Rwork0.2126 --
obs0.2151 13589 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1854 0 46 38 1938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041939
X-RAY DIFFRACTIONf_angle_d0.6242626
X-RAY DIFFRACTIONf_dihedral_angle_d19.885692
X-RAY DIFFRACTIONf_chiral_restr0.041289
X-RAY DIFFRACTIONf_plane_restr0.005329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.430.38571310.33712492X-RAY DIFFRACTION99
2.43-2.680.36391340.29282551X-RAY DIFFRACTION100
2.68-3.060.30651350.24842550X-RAY DIFFRACTION100
3.07-3.860.22471360.19722590X-RAY DIFFRACTION100
3.86-44.540.23751440.18062726X-RAY DIFFRACTION100

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