9y9n

PLK4 in complex with Compound 25 ((R)-7-hydroxy-N-(3-(1-(2,2,2-trifluoroethyl)-1H-pyrazolo[4,3-c]pyridin-6-yl)-1H-pyrazol-4-yl)-7-(trifluoromethyl)-4-azaspiro[2.5]octane-4-carboxamide)

Method: X-RAY DIFFRACTION D_max: 62.9 Å Quality: GOOD

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

Serine/threonine-protein kinase PLK4

Homo sapiens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 4–269	Not recorded	A1CTV (7R)-7-hydroxy-N-{(5P)-5-[1-(2,2,2-trifluoroethyl)-1H-pyrazolo[4,3-c]pyridin-6-yl]-1H-pyrazol-4-yl}-7-(trifluoromethyl)-4-azaspiro[2.5]octane-4-carboxamide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；293 K；1.4 M sodium phosphate monobasic monohydrate/potassium phosphate dibasic pH 5.6	Resolution 1.81 Å R-free 0.237

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.

Other PDB	Difference from Current Entry 9Y9N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2N19 STIL binding to the Polo-box domain 3 of PLK4 regulates centriole duplication Deposited 2015-03-24	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；293.15 K；Ionic strength (raw mmCIF value) 0.03；Pressure ambient NMR sample composition 0.6-1.2 M [U-13C; U-15N; U-2H] PLK4-PB3, 20 mM MOPS, 30 mM sodium chloride, 2 mM TCEP, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.6-1.2 M [U-2H,15N,methyl13C/rest-12C-ILV]-PB3 PLK4-PB3, 20 mM MOPS, 30 mM sodium chloride, 2 mM TCEP, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1200 mM [U-2H,15N,13C,methyl13C/1H-ILV]-PB3 PLK4-PB3, 20 mM MOPS, 30 mM sodium chloride, 2 mM TCEP, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 600 mM [U-2H, U-15N] PLK4-PB3, 20 mM MOPS, 30 mM sodium chloride, 2 mM TCEP, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
3COK Crystal structure of PLK4 kinase Deposited 2008-03-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–275（274 aa） Fragment：Protein kinase domain: Residues 2-275	Not recorded	SO4 SULFATE ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；294 K；100mM Sodium citrate pH 6.0, 16% PEG 4000, 200mM Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.25 Å R-free 0.261
3COK Crystal structure of PLK4 kinase Deposited 2008-03-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–275（274 aa） Fragment：Protein kinase domain: Residues 2-275	Not recorded	SO4 SULFATE ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；294 K；100mM Sodium citrate pH 6.0, 16% PEG 4000, 200mM Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.25 Å R-free 0.261
4JXF Crystal Structure of PLK4 Kinase with an inhibitor: 400631 ((1R,2S)-2-{3-[(E)-2-{4-[(DIMETHYLAMINO)METHYL]PHENYL}ETHENYL]-2H-INDAZOL-6-YL}-5'-METHOXYSPIRO[CYCLOPROPANE-1,3'-INDOL]-2'(1'H)-ONE) Deposited 2013-03-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–269（266 aa） Fragment：PLK4 kinase	Not recorded	631 (1R,2S)-2-{3-[(E)-2-{4-[(dimethylamino)methyl]phenyl}ethenyl]-2H-indazol-6-yl}-5'-methoxyspiro[cyclopropane-1,3'-indol]-2'(1'H)-one × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；23% PEG 3350, 0.1 M HEPES pH 7.5 0.16 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.268
4N7V Crystal structure of human Plk4 cryptic polo box (CPB) in complex with a Cep152 N-terminal fragment Deposited 2013-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 580–808（229 aa） Fragment：UNP residues 580-808 Chain B 580–808（229 aa） Fragment：UNP residues 580-808	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295.15 K；22% PEG 4000, 3% Iso-propanol, 0.1M Tris-HCl, 0.2M Lithium Sulfate , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K	Resolution 2.76 Å R-free 0.288
4N7Z Crystal structure of human Plk4 cryptic polo box (CPB) in complex with a Cep192 N-terminal fragment Deposited 2013-10-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 580–808（229 aa） Fragment：UNP residues 580-808	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295.15 K；20% PEG 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K	Resolution 2.85 Å R-free 0.260
4N9J Crystal structure of the cryptic polo box domain of human Plk4 Deposited 2013-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 581–808（228 aa） Fragment：cryptic polo box, UNP residues 580-808 Chain B 581–808（228 aa） Fragment：cryptic polo box, UNP residues 580-808	Not recorded	CL CHLORIDE ION × 6 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；100 mM Bis-Tris (pH 5.5), 2.0 M ammonium sulfate, 1% (v/v) methanol , VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.60 Å R-free 0.249
4YUR Crystal Structure of Plk4 Kinase Domain Bound to Centrinone Deposited 2015-03-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–275（274 aa） Fragment：UNP residues 2-275	Not recorded	4J7 2-({2-fluoro-4-[(2-fluoro-3-nitrobenzyl)sulfonyl]phenyl}sulfanyl)-5-methoxy-N-(3-methyl-1H-pyrazol-5-yl)-6-(morpholin-4-yl)pyrimidin-4-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；297 K；0.1 M HEPES, 0.2 M MgCl2, 30% PEG 400	Resolution 2.65 Å R-free 0.270
4YYP Crystal structure of human PLK4-PB3 in complex with STIL-CC Deposited 2015-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 884–970（87 aa） Fragment：residues 884-970	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Thin needles grew in precipitant solution containing 100 mM Hepes, pH 7.0, 20 mM MgCl2 and 22% Poly(acrylic acid sodium salt) 5100. After extensive optimization and seeding plate-like crystals were grown in a drop consisting of 50% PLK4-PB3/STIL-CC complex solution, 33.3% precipitant solution (100 mM phosphate/citrate pH 4.2, 40% (v/v) Ethanol, 5% (w/v) PEG 1000) and 16.7% of seed stock solution.	Resolution 2.60 Å R-free 0.254
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 884–970（87 aa） Fragment：UNP residues 884-970 Chain B 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain S 884–970（87 aa） Fragment：UNP residues 884-970 Chain T 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 11 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain U 884–970（87 aa） Fragment：UNP residues 884-970 Chain V 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 12 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain W 884–970（87 aa） Fragment：UNP residues 884-970 Chain X 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 13 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain Y 884–970（87 aa） Fragment：UNP residues 884-970 Chain Z 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 14 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 1 884–970（87 aa） Fragment：UNP residues 884-970 Chain 2 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 15 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 3 884–970（87 aa） Fragment：UNP residues 884-970 Chain 4 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 16 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 5 884–970（87 aa） Fragment：UNP residues 884-970 Chain 6 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 17 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 7 884–970（87 aa） Fragment：UNP residues 884-970 Chain 8 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 18 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 9 884–970（87 aa） Fragment：UNP residues 884-970 Chain a 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 19 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain b 884–970（87 aa） Fragment：UNP residues 884-970 Chain c 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 884–970（87 aa） Fragment：UNP residues 884-970 Chain D 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 20 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain d 884–970（87 aa） Fragment：UNP residues 884-970 Chain e 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 21 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain f 884–970（87 aa） Fragment：UNP residues 884-970 Chain g 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 22 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain h 884–970（87 aa） Fragment：UNP residues 884-970 Chain i 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 23 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain j 884–970（87 aa） Fragment：UNP residues 884-970 Chain k 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 24 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain l 884–970（87 aa） Fragment：UNP residues 884-970 Chain m 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 25 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain n 884–970（87 aa） Fragment：UNP residues 884-970 Chain o 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 26 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain p 884–970（87 aa） Fragment：UNP residues 884-970 Chain q 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 27 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain r 884–970（87 aa） Fragment：UNP residues 884-970 Chain s 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 28 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain t 884–970（87 aa） Fragment：UNP residues 884-970 Chain u 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 29 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain v 884–970（87 aa） Fragment：UNP residues 884-970 Chain w 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 884–970（87 aa） Fragment：UNP residues 884-970 Chain F 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 30 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain x 884–970（87 aa） Fragment：UNP residues 884-970 Chain y 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 884–970（87 aa） Fragment：UNP residues 884-970 Chain H 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain I 884–970（87 aa） Fragment：UNP residues 884-970 Chain J 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain K 884–970（87 aa） Fragment：UNP residues 884-970 Chain L 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain M 884–970（87 aa） Fragment：UNP residues 884-970 Chain N 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain O 884–970（87 aa） Fragment：UNP residues 884-970 Chain P 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHY PB3 Domain of Human PLK4 (apo) Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain Q 884–970（87 aa） Fragment：UNP residues 884-970 Chain R 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)	Resolution 3.31 Å R-free 0.295
5LHZ PB3 Domain of Human PLK4 in Complex with Coiled-Coil Domain of STIL Deposited 2016-07-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；150nl Protein solution (41.87 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 50 nl mother liquor (100mM MES pH 6.0, 191.7 mM Zn acetate, 10% Isopropanol)	Resolution 2.51 Å R-free 0.282
5LHZ PB3 Domain of Human PLK4 in Complex with Coiled-Coil Domain of STIL Deposited 2016-07-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；150nl Protein solution (41.87 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 50 nl mother liquor (100mM MES pH 6.0, 191.7 mM Zn acetate, 10% Isopropanol)	Resolution 2.51 Å R-free 0.282
5LHZ PB3 Domain of Human PLK4 in Complex with Coiled-Coil Domain of STIL Deposited 2016-07-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 884–970（87 aa） Fragment：UNP residues 884-970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；150nl Protein solution (41.87 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 50 nl mother liquor (100mM MES pH 6.0, 191.7 mM Zn acetate, 10% Isopropanol)	Resolution 2.51 Å R-free 0.282
6N45 Crystal structure of the cryptic polo box domain of human activated Plk4 variant 1 Deposited 2018-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 581–808（228 aa） Chain B 581–808（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；4.3M Ammonium Acetate 0.1M BisTris propane pH 8.0	Resolution 2.64 Å R-free 0.314
6N46 Crystal structure of the cryptic polo box domain of a human activated Plk4 Deposited 2018-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 581–808（228 aa） Chain B 581–808（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；281 K；22.5% (w/v) PEG2000 3% (w/v) dextran sulfate sodium salt 0.1M bicine (pH 8.5) 24 uM nonaethylene glycol monododecyl ether (C12E9) 8% (w/v) glycerol	Resolution 3.71 Å R-free 0.309
6N46 Crystal structure of the cryptic polo box domain of a human activated Plk4 Deposited 2018-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 581–808（228 aa） Chain D 581–808（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；281 K；22.5% (w/v) PEG2000 3% (w/v) dextran sulfate sodium salt 0.1M bicine (pH 8.5) 24 uM nonaethylene glycol monododecyl ether (C12E9) 8% (w/v) glycerol	Resolution 3.71 Å R-free 0.309
6N46 Crystal structure of the cryptic polo box domain of a human activated Plk4 Deposited 2018-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 581–808（228 aa） Chain F 581–808（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；281 K；22.5% (w/v) PEG2000 3% (w/v) dextran sulfate sodium salt 0.1M bicine (pH 8.5) 24 uM nonaethylene glycol monododecyl ether (C12E9) 8% (w/v) glycerol	Resolution 3.71 Å R-free 0.309
6N46 Crystal structure of the cryptic polo box domain of a human activated Plk4 Deposited 2018-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 581–808（228 aa） Chain H 581–808（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；281 K；22.5% (w/v) PEG2000 3% (w/v) dextran sulfate sodium salt 0.1M bicine (pH 8.5) 24 uM nonaethylene glycol monododecyl ether (C12E9) 8% (w/v) glycerol	Resolution 3.71 Å R-free 0.309
6W38 Crystal structure of the FAM46C/Plk4 complex Deposited 2020-03-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 585–807（223 aa） Fragment：UNP residues 585-807	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions SMALL TUBES；pH 10；293 K；0.2 M Tris, pH 10	Resolution 4.48 Å R-free 0.295
6W3I Crystal structure of a FAM46C mutant in complex with Plk4 Deposited 2020-03-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 585–807（223 aa） Fragment：UNP residues 585-807	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25% v/v pentaerythritol ethoxylate (15/4 EO/OH), 0.05 M ammonium sulfate, 0.05 M Bis-Tris, pH 6.0	Resolution 3.80 Å R-free 0.261
6W3J Crystal structure of the FAM46C/Plk4/Cep192 complex Deposited 2020-03-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 585–807（223 aa） Fragment：UNP residues 585-807	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions SMALL TUBES；pH 10；293 K；0.2 M Tris, pH 10	Resolution 4.38 Å R-free 0.314
8XPG The Crystal Structure of polo box domain of Plk4 from Biortus. Deposited 2024-01-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 581–808（228 aa） Chain B 581–808（228 aa）	Not recorded	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.00M Ammonium sulfate, 100mM TRIS, pH7.0, 200mM Lithium sulfate	Resolution 2.70 Å R-free 0.260
9O63 Crystal structure of PLK4 and RP1664 complex Deposited 2025-04-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–275（274 aa）	Not recorded	SO4 SULFATE ION × 2 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 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；9 - 14% PEG4K, 0.1 M Na Cit; pH 5.4 - 5.5, 0.2 M (NH4)2SO4	Resolution 2.26 Å R-free 0.264
9Y9B PLK4 in complex with Compound 6 (3-hydroxy-N-(3-(pyridin-2-yl)-1H-pyrazol-4-yl)-8-azabicyclo[3.2.1]octane-8-carboxamide) Deposited 2025-09-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–275（274 aa）	Not recorded	SO4 SULFATE ION × 1 A1CTX (1R,3r,5S)-3-hydroxy-N-[3-(pyridin-2-yl)-1H-pyrazol-4-yl]-8-azabicyclo[3.2.1]octane-8-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；293 K；0.1 M Tris pH 8.5, 16% ethanol , 5 mM DTT	Resolution 2.70 Å R-free 0.335

18 other PDB entries and 53 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PLK4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–266； UniProt 4–269

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9y9n
Deposition date deposition_date	2025-09-14
最后修订 last_revision	2026-02-18
Structure title title	PLK4 in complex with Compound 25 ((R)-7-hydroxy-N-(3-(1-(2,2,2-trifluoroethyl)-1H-pyrazolo[4,3-c]pyridin-6-yl)-1H-pyrazol-4-yl)-7-(trifluoromethyl)-4-azaspiro[2.5]octane-4-carboxamide)
Keywords keywords	PLK4, type 1 inhibitor, SBDD, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	19.51 Å
Radius of gyration Rg (electron density) rg_electron	18.63 Å
Forward intensity I(0) i0	12392000.00
Molecular weight molecular_weight	26470.0 kDa
Excluded volume excluded_volume	33130 Å³
Envelope volume envelope_volume	38076 Å³
Hydration-shell volume shell_volume	17488 Å³
Envelope diameter envelope_diameter	64.4 Å
Shell Rg shell_rg	24.46 Å
Envelope Rg envelope_rg	18.92 Å
Shape Rg shape_rg	18.67 Å
Total Rg total_rg	19.37 Å
Total atoms total_atoms	3681
Residues n_residues	226
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	62.9 Å
Rg (real space) rg_real	19.50 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	1.2390e+07
I(0) uncertainty (real space) i0_real_error	1.4670e+05
Rg (reciprocal space) rg_reciprocal	19.50 Å
I(0) (reciprocal space) i0_reciprocal	12390000.0000
Solution quality estimate total_estimate	0.8104
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.0 Å
Skewness Skewness skewness	0.361
Kurtosis Kurtosis kurtosis	-0.291
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3508000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Serine/threonine-protein kinase PLK4
Molecular weight formula_weight	30530.4 kDa
EC 编号 ec_number	2.7.11.21
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3834

CIGEKIEDFKVGNLLGKGSFAGVYRAESIHTGLEVAIKMIDKKAMYKAGMVQRVQNEVKIHCQLKHPSILELYNYFEDSNYVYLVLEMCHNGEMNRYLKNRVKPFSENEARHFMHQIITGMLYLHSHGILHRDLTLSNLLLTRNMNIKIADFGLATQLKMPHEKHYDLCGTPNYISPEIATRSAHGLESDVWSLGCMFYTLLIGRPPFDTDTVKNTLNKVVLADYEMPSFLSIEAKDLIHQLLRRNPADRLSLSSVLDHPFMSRNS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;(7R)-7-hydroxy-N-{(5P)-5-[1-(2,2,2-trifluoroethyl)-1H-pyrazolo[4,3-c]pyridin-6-yl]-1H-pyrazol-4-yl}-7-(trifluoromethyl)-4-azaspiro[2.5]octane-4-carboxamide ;
Molecular weight formula_weight	503.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

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8. Citations (1)

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Unit-cell length a length_a	105.097 Å
Unit-cell length b length_b	105.097 Å
Unit-cell length c length_c	47.974 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	1.810 Å
Low-resolution limit resolution_low	23.200 Å
R factor r_factor	0.2094
R_work r_work	0.2080
R_free r_free	0.2372

fit	/app/data/saxs_computation/y9/9y9n/9y9n.fit
pddf	/app/data/pr_computation/y9/9y9n/9y9n.pr.out
profile	/app/data/saxs_computation/y9/9y9n/9y9n.dat