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9d0q

Crystal structure of human Wee1 kinase domain in complex with inhibitor

Method: X-RAY DIFFRACTION Dmax: 91.3 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Wee1-like protein kinase

Homo sapiens

UniProt P30291

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 291–575 Not recorded A1A1S 1-[(6R)-6-(2,6-dichlorophenyl)-8-methyl-2-[4-(4-methylpiperazin-1-yl)anilino]-7,8-dihydropteridin-5(6H)-yl]ethan-1-one × 1 NA SODIUM ION × 1 CL CHLORIDE ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；hepes, sodiium chloride, pH 7.5 Resolution 1.96 Å R-free 0.270
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 291–575 Not recorded A1A1S 1-[(6R)-6-(2,6-dichlorophenyl)-8-methyl-2-[4-(4-methylpiperazin-1-yl)anilino]-7,8-dihydropteridin-5(6H)-yl]ethan-1-one × 1 NA SODIUM ION × 1 CL CHLORIDE ION × 9 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；hepes, sodiium chloride, pH 7.5 Resolution 1.96 Å R-free 0.270

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 9D0Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1X8B Structure of human Wee1A kinase: kinase domain complexed with inhibitor PD0407824 Deposited 2004-08-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa） Fragment：kinase domain
Not recorded MG MAGNESIUM ION × 2 824 9-HYDROXY-4-PHENYLPYRROLO[3,4-C]CARBAZOLE-1,3(2H,6H)-DIONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES, sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.81 Å R-free 0.237
2IN6 Wee1 kinase complex with inhibitor PD311839 Deposited 2006-10-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa） Fragment：kinase domain
Not recorded 839 3-(9-HYDROXY-1,3-DIOXO-4-PHENYL-2,3-DIHYDROPYRROLO[3,4-C]CARBAZOL-6(1H)-YL)PROPANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES, sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.299
2IO6 Wee1 kinase complexed with inhibitor PD330961 Deposited 2006-10-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa） Fragment：kinase domain
Not recorded 330 9-HYDROXY-6-(3-HYDROXYPROPYL)-4-(2-METHOXYPHENYL)PYRROLO[3,4-C]CARBAZOLE-1,3(2H,6H)-DIONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES, sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.273
2Z2W Human Wee1 kinase complexed with inhibitor PF0335770 Deposited 2007-05-29 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 291–575（285 aa） Fragment：kinase domain
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 770 N-[4-(2-CHLOROPHENYL)-1,3-DIOXO-1,2,3,6-TETRAHYDROPYRROLO[3,4-C]CARBAZOL-9-YL]FORMAMIDE × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；NaCL, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.22 Å R-free 0.271
2Z2W Human Wee1 kinase complexed with inhibitor PF0335770 Deposited 2007-05-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa） Fragment：kinase domain
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 1 770 N-[4-(2-CHLOROPHENYL)-1,3-DIOXO-1,2,3,6-TETRAHYDROPYRROLO[3,4-C]CARBAZOL-9-YL]FORMAMIDE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；NaCL, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.22 Å R-free 0.271
3BI6 Wee1 kinase complex with inhibitor PD352396 Deposited 2007-11-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa） Fragment：kinase domain
Not recorded CL CHLORIDE ION × 1 396 4-(2-chlorophenyl)-9-hydroxy-6-methyl-1,3-dioxo-N-(2-pyrrolidin-1-ylethyl)pyrrolo[3,4-g]carbazole-8-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES, NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.251
3BIZ Wee1 kinase complex with inhibitor PD331618 Deposited 2007-12-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa） Fragment：kinase domain
Not recorded CL CHLORIDE ION × 1 61E 4-(2-chlorophenyl)-8-[3-(dimethylamino)propoxy]-9-hydroxy-6-methylpyrrolo[3,4-c]carbazole-1,3(2H,6H)-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES, NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.247
3CQE Wee1 kinase complex with inhibitor PD074291 Deposited 2008-04-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa） Fragment：kinase domain
Not recorded CL CHLORIDE ION × 1 P91 8-bromo-4-(2-chlorophenyl)-N-(2-hydroxyethyl)-6-methyl-1,3-dioxo-1,2,3,6-tetrahydropyrrolo[3,4-e]indole-7-carboxamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HEPES, sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP
Resolution 2.50 Å R-free 0.268
3CR0 Wee1 kinase complex with inhibitor PD259_809 Deposited 2008-04-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa） Fragment：kinase domain
Not recorded CL CHLORIDE ION × 1 809 4-(2-chlorophenyl)-8-(2-hydroxyethyl)-6-methylpyrrolo[3,4-e]indole-1,3(2H,6H)-dione × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES, sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.255
5V5Y CRYSTAL STRUCTURE OF HUMAN WEE1 KINASE DOMAIN IN COMPLEX WITH MK1775 Deposited 2017-03-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa） Fragment：UNP RESIDUES 291-575
Not recorded 8X7 1-[6-(2-hydroxypropan-2-yl)pyridin-2-yl]-6-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one × 1 DMS DIMETHYL SULFOXIDE × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；9.0 MG/ML WEE1, 25 mM Na/K phosphate, 1 mM DTT, 0.1 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5), 12.5 % PEG 3350, 1 mM MK1775
Resolution 1.90 Å R-free 0.215
5VC3 CRYSTAL STRUCTURE OF HUMAN WEE1 KINASE DOMAIN IN COMPLEX WITH BOSUTINIB Deposited 2017-03-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa） Fragment：UNP RESIDUES 291-575
Not recorded DB8 4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile × 1 EDO 1,2-ETHANEDIOL × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；5.0 MG/ML WEE1, 25 mM Na/K phosphate, 1 mM DTT, 0.05 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5),7.5 % PEG 3350, 1 mM Bosutinib
Resolution 1.97 Å R-free 0.254
5VC4 Crystal structure of HUMAN WEE1 KINASE domain in complex with Bosutinib-isomer Deposited 2017-03-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa） Fragment：UNP RESIDUES 291-575
Mutation：NONE XZN 4-[(3,5-DICHLORO-4-METHOXYPHENYL)AMINO]-6-METHOXY-7-[3-(4-METHYLPIPERAZIN-1-YL)PROPOXY]QUINOLINE-3-CARBONITRILE × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；5.0 MG/ML WEE1, 25 mM Na/K phosphate, 1 mM DTT, 0.05 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5), 7.5 % PEG 3350, 1 mM Bosutinib-isomer
Resolution 2.10 Å R-free 0.241
5VC5 Crystal structure of human WEE1 kinase domain in complex with PD-166285 Deposited 2017-03-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa） Fragment：UNP RESIDUES 291-575
Not recorded 96M 6-(2,6-dichlorophenyl)-2-({4-[2-(diethylamino)ethoxy]phenyl}amino)-8-methylpyrido[2,3-d]pyrimidin-7(8H)-one × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；9.0 MG/ML WEE1, 25 mM Na/K phosphate, 1 mM DTT, 0.05 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5), 7.5 % PEG 3350, 1 mM PD-166285
Resolution 1.93 Å R-free 0.217
5VC6 crystal structure of human WEE1 kinase domain in complex with PHA-848125 Deposited 2017-03-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa） Fragment：UNP RESIDUES 291-575
Not recorded P48 N,1,4,4-TETRAMETHYL-8-{[4-(4-METHYLPIPERAZIN-1-YL)PHENYL]AMINO}-4,5-DIHYDRO-1H-PYRAZOLO[4,3-H]QUINAZOLINE-3-CARBOXAMIDE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；5.0 MG/ML WEE1, 25 mM Na/K phosphate, 1 mM DTT, 0.05 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5), 7.5 % PEG 3350, 1 mM PHA-848125
Resolution 2.00 Å R-free 0.265
5VD2 crystal structure of human WEE1 kinase domain in complex with PF-03814735 Deposited 2017-04-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa） Fragment：UNP RESIDUES 291-575
Not recorded 34W N-{2-[(1S,4R)-6-{[4-(cyclobutylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}-1,2,3,4-tetrahydro-1,4-epiminonaphthalen-9-yl]-2-oxoethyl}acetamide × 1 PO4 PHOSPHATE ION × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；9.0 MG/ML WEE1, 25 mM Na/K phosphate, 1 mM DTT, 0.05 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5), 7.5 % PEG 3350, 1 mM PF-03814735
Resolution 2.05 Å R-free 0.256
5VD4 CRYSTAL STRUCTURE OF HUMAN WEE1 KINASE DOMAIN IN COMPLEX WITH RAC-IV-016, a MK1775 analougue Deposited 2017-04-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa） Fragment：UNP RESIDUES 291-575
Not recorded 99J 6-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-2-(prop-2-en-1-yl)-1-{6-[(1S)-2,2,2-trifluoro-1-hydroxyethyl]pyridin-2-yl}-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one × 1 PO4 PHOSPHATE ION × 2 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；5.0 MG/ML WEE1, 25 mM Na/K phosphate, 1 mM DTT, 0.05 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5), 7.5 % PEG 3350, 1 mM RAC-IV-016
Resolution 2.02 Å R-free 0.245
5VD5 CRYSTAL STRUCTURE OF HUMAN WEE1 KINASE DOMAIN IN COMPLEX WITH RAC-IV-050, a MK1775 analougue Deposited 2017-04-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa） Fragment：UNP RESIDUES 291-575
Not recorded 99M 1-[6-(2-hydroxypropan-2-yl)pyridin-2-yl]-6-{[4-(morpholin-4-yl)phenyl]amino}-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo [3,4-d]pyrimidin-3-one × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；5.0 MG/ML WEE1, 25 mM Na/K phosphate, 1 mM DTT, 0.05 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5), 7.5 % PEG 3350, 1 mM RAC-IV-050
Resolution 2.05 Å R-free 0.234
5VD7 CRYSTAL STRUCTURE OF HUMAN WEE1 KINASE DOMAIN IN COMPLEX WITH RAC-IV-098, a MK1775 analogue Deposited 2017-04-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa） Fragment：UNP RESIDUES 291-575
Not recorded 99V 6-{[3-fluoro-4-(4-methylpiperazin-1-yl)phenyl]amino}-1-[6-(2-hydroxypropan-2-yl)pyridin-2-yl]-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；5.0 MG/ML WEE1, 25 mM Na/K phosphate, 1 mM DTT, 0.05 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5), 7.5 % PEG 3350, 1 mM RAC-IV-098
Resolution 2.08 Å R-free 0.248
5VD8 Crystal structure of human WEE1 kinase domain in complex with RAC-IV-099, a MK1775 analogue Deposited 2017-04-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa） Fragment：UNP RESIDUES 291-575
Not recorded 98M 6-{[3-chloro-4-(4-methylpiperazin-1-yl)phenyl]amino}-1-[6-(2-hydroxypropan-2-yl)pyridin-2-yl]-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；5.0 MG/ML WEE1, 25 mM Na/K phosphate, 1 mM DTT, 0.05 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5), 7.5 % PEG 3350, 1 mM RAC-IV-099
Resolution 1.85 Å R-free 0.247
5VD9 Crystal structure of human WEE1 kinase domain in complex with RAC-IV-097, a MK1775 analogue Deposited 2017-04-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa） Fragment：UNP RESIDUES 291-575
Not recorded 98G 1-{6-[(1R)-1-hydroxyethyl]pyridin-2-yl}-6-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；5.0 MG/ML WEE1, 25 mM Na/K phosphate, 1 mM DTT, 0.05 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5), 7.5 % PEG 3350, 1 mM RAC-IV-097
Resolution 1.87 Å R-free 0.253
5VDA Crystal structure of human WEE1 kinase domain in complex with RAC-IV-101, a MK1775 analogue Deposited 2017-04-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa） Fragment：UNP RESIDUES 291-575
Not recorded 98D 1-{6-[(1S)-1-hydroxyethyl]pyridin-2-yl}-6-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；5.0 MG/ML WEE1, 25 mM Na/K phosphate, 1 mM DTT, 0.05 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5), 7.5 % PEG 3350, 1 mM RAC-IV-101
Resolution 2.10 Å R-free 0.255
7N3U Crystal structure of human WEE1 kinase domain in complex with ZN-c3 Deposited 2021-06-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa）
Not recorded 05J 1-[(7R)-7-ethyl-7-hydroxy-6,7-dihydro-5H-cyclopenta[b]pyridin-2-yl]-6-[4-(4-methylpiperazin-1-yl)anilino]-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291.15 K；20% PEG 20K
Resolution 2.65 Å R-free 0.267
8BJU HUMAN WEE1 KINASE IN COMPLEX WITH INHIBITOR 1-[6-(1-Hydroxy-1-methyl-ethyl)-pyridin-2-yl]-2-(2-methoxy-phenyl)-6-[4-(4-methyl-piperazin-1-yl)-phenylamino]-1,2-dihydro-pyrazolo[3,4-d]pyrimidin-3-one Deposited 2022-11-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa）
Not recorded QT9 2-(2-methoxyphenyl)-6-[[4-(4-methylpiperazin-1-yl)phenyl]amino]-1-[6-(2-oxidanylpropan-2-yl)pyridin-2-yl]pyrazolo[3,4-d]pyrimidin-3-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.75；277 K；6.0 % w/v PEG6000, 0.10M MES pH 4.75
Resolution 1.53 Å R-free 0.263
8WDK The complex structure of Cul2-VCB-Protac-Wee1 Deposited 2023-09-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain W 291–575（285 aa）
Not recorded W6U (2S,4R)-1-[(2S)-3,3-dimethyl-2-[3-[4-[4-[4-[[3-oxidanylidene-1-[6-(2-oxidanylpropan-2-yl)pyridin-2-yl]-2-prop-2-enyl-pyrazolo[3,4-d]pyrimidin-6-yl]amino]phenyl]piperazin-1-yl]butoxy]propanoylamino]butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.64 Å
9D0R Crystal structure of human Wee1 kinase domain in complex with inhibitor Deposited 2024-08-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa）
Not recorded NA SODIUM ION × 1 CL CHLORIDE ION × 5 A1A1T 7-methyl-2-{[1-(1-methylpiperidin-4-yl)-1H-pyrazol-4-yl]amino}-6-[(1R)-1-(thiophen-2-yl)ethyl]-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；hepes, sodium chloride, pH 7.5
Resolution 2.34 Å R-free 0.256
9D0S Crystal structure of human Wee1 kinase domain in complex with inhibitor Deposited 2024-08-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 291–575（285 aa）
Not recorded NA SODIUM ION × 1 CL CHLORIDE ION × 13 A1A1R (8P)-3-(2,6-dichlorophenyl)-1-methyl-8-[1-(1-methylpiperidin-4-yl)-1H-pyrazol-4-yl]-1,2,3,7-tetrahydro-4H-pyrrolo[3',2':5,6]pyrido[4,3-d]pyrimidin-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；hepes, sodium chloride, pH 7.5
Resolution 1.64 Å R-free 0.222
9R55 Wee1-like kinase in complex wirh MIPS-54859 Deposited 2025-05-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 292–575（284 aa）
Not recorded A1JDB MIPS-54859 × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；20% w/v PEG 8000, 0.2 M Magnesium acetate tetrahydrate, 0.1M Sodium cacodylate, pH 6.5
Resolution 2.67 Å R-free 0.264
9R55 Wee1-like kinase in complex wirh MIPS-54859 Deposited 2025-05-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 292–575（284 aa）
Not recorded A1JDB MIPS-54859 × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；20% w/v PEG 8000, 0.2 M Magnesium acetate tetrahydrate, 0.1M Sodium cacodylate, pH 6.5
Resolution 2.67 Å R-free 0.264
9R56 Wee1-like kinase in complex wirh MIPS-54861 Deposited 2025-05-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 292–575（284 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 A1JDC MIPS-54861 × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG6000, 10% ethylene glycol, 0.1M MES pH 6.0, 0.2M ammonium chloride
Resolution 3.01 Å R-free 0.292
9R56 Wee1-like kinase in complex wirh MIPS-54861 Deposited 2025-05-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 292–575（284 aa）
Not recorded A1JDC MIPS-54861 × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG6000, 10% ethylene glycol, 0.1M MES pH 6.0, 0.2M ammonium chloride
Resolution 3.01 Å R-free 0.292
9TG7 Crystal structure of beta-TrCP bound by monophosphorylated WEE1 degron peptide Deposited 2025-11-28 Different construct Different mutation/modification 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 49–60（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；20% PEG10K, 0.1 M Na-Hepes pH 7.5
Resolution 1.68 Å R-free 0.252

28 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name WEE1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–289； UniProt 291–575 Author chain B； PDBConstruct 5–289； UniProt 291–575

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 9d0q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9d0q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9d0q
Deposition date deposition_date2024-08-07
最后修订 last_revision2025-09-10
Structure title titleCrystal structure of human Wee1 kinase domain in complex with inhibitor
Keywords keywordstyrosine-protein kinase, kinase, transferase, inhibitor, complex, TRANSFERASE-INHIBITOR complex; TRANSFERASE/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.23 Å
Radius of gyration Rg (electron density) rg_electron28.45 Å
Forward intensity I(0) i067023400.00
Molecular weight molecular_weight63481.0 kDa
Excluded volume excluded_volume79195 ų
Envelope volume envelope_volume100250 ų
Hydration-shell volume shell_volume29750 ų
Envelope diameter envelope_diameter99.5 Å
Shell Rg shell_rg35.35 Å
Envelope Rg envelope_rg28.50 Å
Shape Rg shape_rg28.44 Å
Total Rg total_rg29.18 Å
Total atoms total_atoms8839
Residues n_residues550
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax91.3 Å
Rg (real space) rg_real29.22 Å
Rg uncertainty (real space) rg_real_error0.62 Å
I(0) (real space) i0_real6.7020e+07
I(0) uncertainty (real space) i0_real_error1.1220e+06
Rg (reciprocal space) rg_reciprocal29.23 Å
I(0) (reciprocal space) i0_reciprocal67020000.0000
Solution quality estimate total_estimate0.9084
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.8 Å
Skewness Skewness skewness0.254
Kurtosis Kurtosis kurtosis-0.647
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14470000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.942
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)