5vda

Crystal structure of human WEE1 kinase domain in complex with RAC-IV-101, a MK1775 analogue

Method: X-RAY DIFFRACTION D_max: 63.3 Å Quality: GOOD

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

Wee1-like protein kinase

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 291–575	Fragment：UNP RESIDUES 291-575	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

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 5VDA	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 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 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 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 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 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 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 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 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 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 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 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
7N3U Crystal structure of human WEE1 kinase domain in complex with ZN-c3 Deposited 2021-06-02	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）	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 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）	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 construct 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
9D0Q Crystal structure of human Wee1 kinase domain in complex with inhibitor Deposited 2024-08-07	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）	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
9D0Q Crystal structure of human Wee1 kinase domain in complex with inhibitor Deposited 2024-08-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 291–575（285 aa）	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
9D0R Crystal structure of human Wee1 kinase domain in complex with inhibitor Deposited 2024-08-07	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）	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 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）	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 32 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

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	5vda
Deposition date deposition_date	2017-04-01
Structure title title	Crystal structure of human WEE1 kinase domain in complex with RAC-IV-101, a MK1775 analogue
Keywords keywords	KINASE DOMAIN, CELL CYCLE, WEE1, TRANSFERASE, INHIBITOR, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
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	19.83 Å
Radius of gyration Rg (electron density) rg_electron	18.71 Å
Forward intensity I(0) i0	15881700.00
Molecular weight molecular_weight	29868.0 kDa
Excluded volume excluded_volume	37383 Å³
Envelope volume envelope_volume	43859 Å³
Hydration-shell volume shell_volume	19562 Å³
Envelope diameter envelope_diameter	64.7 Å
Shell Rg shell_rg	25.02 Å
Envelope Rg envelope_rg	18.92 Å
Shape Rg shape_rg	18.69 Å
Total Rg total_rg	19.71 Å
Total atoms total_atoms	4191
Residues n_residues	259
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	63.3 Å
Rg (real space) rg_real	19.74 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	1.5880e+07
I(0) uncertainty (real space) i0_real_error	2.0570e+05
Rg (reciprocal space) rg_reciprocal	19.75 Å
I(0) (reciprocal space) i0_reciprocal	15880000.0000
Solution quality estimate total_estimate	0.8940
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.0 Å
Skewness Skewness skewness	0.247
Kurtosis Kurtosis kurtosis	-0.345
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4812000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.978

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Wee1-like protein kinase
Molecular weight formula_weight	32440.9 kDa
EC 编号 ec_number	2.7.10.2
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	4274

GAGSMKSRYTTEFHELEKIGSGEFGSVFKCVKRLDGCIYAIKRSKKPLAGSVDEQNALREVYAHAVLGQHSHVVRYFSAWAEDDHMLIQNEYCNGGSLADAISENYRIMSYFKEAELKDLLLQVGRGLRYIHSMSLVHMDIKPSNIFISRTSIPNAASEEGDEDDWASNKVMFKIGDLGHVTRISSPQVEEGDSRFLANEVLQENYTHLPKADIFALALTVVCAAGAEPLPRNGDQWHEIRQGRLPRIPQVLSQEFTELLKVMIHPDPERRPSAMALVKHSVLLSASRK

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	;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 ;
Molecular weight formula_weight	486.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	83

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5vdaa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	5vdaA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	5vdaA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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8. Citations (1)

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Unit-cell length a length_a	50.360 Å
Unit-cell length b length_b	44.640 Å
Unit-cell length c length_c	64.620 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.18 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	63.164 Å
R factor r_factor	—
R_work r_work	0.1906
R_free r_free	0.2554

fit	/app/data/saxs_computation/vd/5vda/5vda.fit
pddf	/app/data/pr_computation/vd/5vda/5vda.pr.out
profile	/app/data/saxs_computation/vd/5vda/5vda.dat