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23es

Crystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 11

Method: X-RAY DIFFRACTION Dmax: 79.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase

Homo sapiens

UniProt Q99640

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 76–361 Not recorded A1E5A 3-azanyl-5-chloranyl-4-(7-fluoranyl-2H-indazol-4-yl)-7-methyl-1H-1,6-naphthyridin-2-one × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.1 M CALCIUM CHLORIDE, 0.05 M TRIS pH 8.5, 10 % PEG 4000 Resolution 1.74 Å R-free 0.240
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 76–361 Not recorded A1E5A 3-azanyl-5-chloranyl-4-(7-fluoranyl-2H-indazol-4-yl)-7-methyl-1H-1,6-naphthyridin-2-one × 1 SO4 SULFATE ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.1 M CALCIUM CHLORIDE, 0.05 M TRIS pH 8.5, 10 % PEG 4000 Resolution 1.74 Å R-free 0.240

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 23ES Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
13LV Structure of PKMYT1 bound to allosteric inhibitor P29-(S) Deposited 2026-05-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–362（288 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.22 Å R-free 0.269
13LW Structure of PKMYT1 bound to inhibitor P32-(S) Deposited 2026-05-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–362（288 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.95 Å R-free 0.247
13LX Structure of PKMYT1 bound to inhibitor P32-(R) Deposited 2026-05-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–362（288 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å R-free 0.280
23FW Crystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 16 Deposited 2026-02-05 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 76–361（286 aa）
Not recorded A1E5J 9-azanyl-10-(7-fluoranyl-1H-indazol-4-yl)-6-methyl-2,3,4,7-tetrahydropyrano[2,3-f][1,7]naphthyridin-8-one × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.1 M CALCIUM CHLORIDE, 0.05 M TRIS pH 8.5, 10 % PEG 4000
Resolution 1.59 Å R-free 0.195
23FW Crystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 16 Deposited 2026-02-05 Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 76–361（286 aa）
Not recorded A1E5J 9-azanyl-10-(7-fluoranyl-1H-indazol-4-yl)-6-methyl-2,3,4,7-tetrahydropyrano[2,3-f][1,7]naphthyridin-8-one × 1 EDO 1,2-ETHANEDIOL × 5 SO4 SULFATE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.1 M CALCIUM CHLORIDE, 0.05 M TRIS pH 8.5, 10 % PEG 4000
Resolution 1.59 Å R-free 0.195
3P1A Structure of human Membrane-associated Tyrosine- and Threonine-specific cdc2-inhibitory kinase MYT1 (PKMYT1) Deposited 2010-09-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–362（288 aa） Fragment：kinase domain, UNP residue 75-362
Not recorded EDO 1,2-ETHANEDIOL × 10 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；20% PEG 3350, 0.2M KSCN, 0.1M Bis-Tris Propane, pH 6.5, 10% Ethylene glycol , VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 1.70 Å R-free 0.195
5VCV CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH Dasatinib Deposited 2017-04-01 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 75–362（288 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 75-362
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 1 1N1 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.1 M CALCIUM CHLORIDE, 0.05 M TRIS pH 8.5, 10 % PEG 4000, 1 mM Dasatinib
Resolution 1.92 Å R-free 0.197
5VCW CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH Pelitinib 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 75–362（288 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 75-362
Not recorded 93J (2E)-N-{4-[(3-chloro-4-fluorophenyl)amino]-3-cyano-7-ethoxyquinolin-6-yl}-4-(dimethylamino)but-2-enamide × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.05 M MES pH 6.5, 0.8 M Magnesium sulfate, 2 mM Pelitinib
Resolution 2.25 Å R-free 0.246
5VCW CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH Pelitinib Deposited 2017-04-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 75–362（288 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 75-362
Not recorded 93J (2E)-N-{4-[(3-chloro-4-fluorophenyl)amino]-3-cyano-7-ethoxyquinolin-6-yl}-4-(dimethylamino)but-2-enamide × 1 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.05 M MES pH 6.5, 0.8 M Magnesium sulfate, 2 mM Pelitinib
Resolution 2.25 Å R-free 0.246
5VCX CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN (UNTREATED) IN COMPLEX WITH SARACATINIB 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 75–362（288 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 75-362
Not recorded H8H N-(5-CHLORO-1,3-BENZODIOXOL-4-YL)-7-[2-(4-METHYLPIPERAZIN-1-YL)ETHOXY]-5-(TETRAHYDRO-2H-PYRAN-4-YLOXY)QUINAZOLIN-4-AMINE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.1 M CALCIUM CHLORIDE, 0.05 M TRIS pH 8.5, 10 % PEG 4000, 1 mM SARACATINIB
Resolution 2.70 Å R-free 0.244
5VCY CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH BOSUTINIB 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 75–362（288 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 75-362
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 × 3 PEG DI(HYDROXYETHYL)ETHER × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；14 MG/ML MYT1, 50 mM HEPES PH 7.5, 0.5 mM DTT, 0.05 M POTASSIUM CHLORIDE, 17.5 (V/V) % pentaerythritol propoxylate (5/4 PO/OH), 1.5 mM BOSUTINIB
Resolution 1.56 Å R-free 0.178
5VCZ CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH Bosutinib isomer 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 75–362（288 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 75-362
Not recorded XZN 4-[(3,5-DICHLORO-4-METHOXYPHENYL)AMINO]-6-METHOXY-7-[3-(4-METHYLPIPERAZIN-1-YL)PROPOXY]QUINOLINE-3-CARBONITRILE × 1 EDO 1,2-ETHANEDIOL × 5 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；14 MG/ML MYT1, 50 mM HEPES PH 7.5, 0.5 mM DTT, 0.05 M POTASSIUM CHLORIDE, 17.5 (V/V) % pentaerythritol propoxylate (5/4 PO/OH), 1.5 mM osutinib isomer
Resolution 1.50 Å R-free 0.181
5VD0 CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH MK1775 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 75–362（288 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 75-362
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 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；14 MG/ML MYT1, 50 mM HEPES PH 7.5, 0.5 mM DTT, 0.05 M POTASSIUM CHLORIDE, 17.5 (V/V) % pentaerythritol propoxylate (5/4 PO/OH), 1.5 mM MK1775
Resolution 2.13 Å R-free 0.231
5VD1 CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH PHA-848125 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 75–362（288 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 75-362
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 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；14 MG/ML MYT1, 50 mM HEPES PH 7.5, 0.5 mM DTT, 0.05 M POTASSIUM CHLORIDE, 17.5 (V/V) % pentaerythritol propoxylate (5/4 PO/OH), 1.5 mM PHA-848125
Resolution 1.70 Å R-free 0.194
5VD3 CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN (de-phosphorylated) IN COMPLEX WITH SARACATINIB 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 75–362（288 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 75-362
Not recorded H8H N-(5-CHLORO-1,3-BENZODIOXOL-4-YL)-7-[2-(4-METHYLPIPERAZIN-1-YL)ETHOXY]-5-(TETRAHYDRO-2H-PYRAN-4-YLOXY)QUINAZOLIN-4-AMINE × 1 EDO 1,2-ETHANEDIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；14 MG/ML MYT1, 50 mM HEPES PH 7.5, 0.5 mM DTT, 0.05 M POTASSIUM CHLORIDE, 17.5 (V/V) % pentaerythritol propoxylate (5/4 PO/OH), 1.5 mM SARACATINIB
Resolution 1.80 Å R-free 0.204
8D6C Crystal Structure of Human Myt1 Kinase domain Bounded with compound 28 Deposited 2022-06-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–362（288 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 75-362
Not recorded EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 1 QGR (1P)-2-amino-6-bromo-1-(3-hydroxy-2,6-dimethylphenyl)-1H-pyrrolo[2,3-b]quinoxaline-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.25；293 K；5.6 to 6.6 % PEG3350, 0.2 M Na2SO4, 0.1 M Tris-HCl and 10% EG
Resolution 2.20 Å R-free 0.267
8D6C Crystal Structure of Human Myt1 Kinase domain Bounded with compound 28 Deposited 2022-06-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 75–362（288 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 75-362
Not recorded EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 1 QGR (1P)-2-amino-6-bromo-1-(3-hydroxy-2,6-dimethylphenyl)-1H-pyrrolo[2,3-b]quinoxaline-3-carboxamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.25；293 K；5.6 to 6.6 % PEG3350, 0.2 M Na2SO4, 0.1 M Tris-HCl and 10% EG
Resolution 2.20 Å R-free 0.267
8D6D Crystal Structure of Human Myt1 Kinase domain Bounded with compound 39 Deposited 2022-06-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–362（288 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 75-362
Not recorded EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 1 QGY (1P)-2-amino-5-bromo-1-(3-hydroxy-2,6-dimethylphenyl)-1H-pyrrolo[2,3-b]quinoxaline-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.25；293 K；5.6 to 6.6% PEG3350, 0.2 M Na2SO4, 0.1 M Tris-HCl and 10% EG
Resolution 2.35 Å R-free 0.272
8D6D Crystal Structure of Human Myt1 Kinase domain Bounded with compound 39 Deposited 2022-06-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 75–362（288 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 75-362
Not recorded EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 1 QGY (1P)-2-amino-5-bromo-1-(3-hydroxy-2,6-dimethylphenyl)-1H-pyrrolo[2,3-b]quinoxaline-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.25；293 K；5.6 to 6.6% PEG3350, 0.2 M Na2SO4, 0.1 M Tris-HCl and 10% EG
Resolution 2.35 Å R-free 0.272
8D6E Crystal Structure of Human Myt1 Kinase domain Bounded with RP-6306 Deposited 2022-06-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 75–362（288 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 75-362
Not recorded SO4 SULFATE ION × 1 QGI (1P)-2-amino-1-(3-hydroxy-2,6-dimethylphenyl)-5,6-dimethyl-1H-pyrrolo[2,3-b]pyridine-3-carboxamide × 1 GOL GLYCEROL × 3 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.25；293 K；5.6 to 6.6% PEG3350, 0.2 M Na2SO4, 0.1 M Tris-HCl and 10% EG
Resolution 2.15 Å R-free 0.218
8D6E Crystal Structure of Human Myt1 Kinase domain Bounded with RP-6306 Deposited 2022-06-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–362（288 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 75-362
Not recorded SO4 SULFATE ION × 1 QGI (1P)-2-amino-1-(3-hydroxy-2,6-dimethylphenyl)-5,6-dimethyl-1H-pyrrolo[2,3-b]pyridine-3-carboxamide × 1 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.25；293 K；5.6 to 6.6% PEG3350, 0.2 M Na2SO4, 0.1 M Tris-HCl and 10% EG
Resolution 2.15 Å R-free 0.218
8D6F Crystal Structure of Human Myt1 Kinase domain Bounded with Eph receptor inhibitor / compound 41 Deposited 2022-06-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 75–362（288 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 75-362
Not recorded SO4 SULFATE ION × 1 QG5 (1M)-2-amino-1-(5-hydroxy-2-methylphenyl)-1H-pyrrolo[2,3-b]quinoxaline-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.25；293 K；5.6 to 6.6% PEG3350, 0.2 M Na2SO4, 0.1 M Tris-HCl and 10% EG
Resolution 2.49 Å R-free 0.239
8D6F Crystal Structure of Human Myt1 Kinase domain Bounded with Eph receptor inhibitor / compound 41 Deposited 2022-06-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–362（288 aa） Fragment：KINASE DOMAIN, UNP RESIDUES 75-362
Not recorded SO4 SULFATE ION × 1 QG5 (1M)-2-amino-1-(5-hydroxy-2-methylphenyl)-1H-pyrrolo[2,3-b]quinoxaline-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.25；293 K；5.6 to 6.6% PEG3350, 0.2 M Na2SO4, 0.1 M Tris-HCl and 10% EG
Resolution 2.49 Å R-free 0.239
8WJY PKMYT1_Cocrystal_Cpd 4 Deposited 2023-09-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–362（288 aa）
Not recorded W9X [6-azanyl-5-(2,6-dimethyl-3-oxidanyl-phenyl)-2,3-dimethyl-pyrrolo[2,3-b]pyrazin-7-yl]-(6,7-dihydro-4~{H}-pyrazolo[1,5-a]pyrazin-5-yl)methanone × 1 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；SM5-E1+30%Gly
Resolution 1.88 Å R-free 0.217
8ZTX Crystal Structure of Human Myt1 Kinase domain Bounded with compound 6b Deposited 2024-06-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–362（288 aa）
Not recorded A1D83 2-azanyl-3-(2,6-dimethyl-3-oxidanyl-phenyl)-5-pyridin-4-yl-benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.8 M Ammonium sulfate,100 mM Sodium citrate,pH 5.5
Resolution 1.70 Å R-free 0.216
8ZU2 Crystal Structure of Human Myt1 Kinase domain Bounded with compound 8g Deposited 2024-06-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–361（287 aa）
Not recorded GLY GLYCINE × 1 A1D85 2-azanyl-5-[2-(1,4-diazepan-1-yl)pyridin-4-yl]-3-(2,6-dimethyl-3-oxidanyl-phenyl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；0.8 M Ammonium sulfate,100 mM Sodium citrate,pH 5.5
Resolution 1.80 Å R-free 0.222
8ZUD Crystal Structure of Human Myt1 Kinase domain Bounded with compound 8f Deposited 2024-06-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–361（287 aa）
Not recorded A1D82 2-azanyl-3-(2,6-dimethyl-3-oxidanyl-phenyl)-5-(2-morpholin-4-ylpyridin-4-yl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.8 M Ammonium sulfate,100 mM Sodium citrate,pH 6.5
Resolution 1.51 Å R-free 0.238
8ZUL Crystal Structure of Human Myt1 Kinase domain Bounded with compound 8m Deposited 2024-06-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–361（287 aa）
Not recorded A1D84 2-azanyl-5-[2-[(3~{R})-3-azanylpyrrolidin-1-yl]pyridin-4-yl]-3-(2,6-dimethyl-3-oxidanyl-phenyl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；0.8 M Ammonium sulfate,100 mM Sodium citrate,pH 5.5
Resolution 1.80 Å R-free 0.219
9LGL Crystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 6 Deposited 2025-01-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–361（287 aa）
Not recorded A1EJW 3-azanyl-7-chloranyl-4-(2-methyl-5-oxidanyl-phenyl)-1H-1,5-naphthyridin-2-one × 1 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.1 M CALCIUM CHLORIDE, 0.05 M TRIS pH 8.5, 10 % PEG 4000
Resolution 2.17 Å R-free 0.234
9LGL Crystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 6 Deposited 2025-01-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 75–361（287 aa）
Not recorded A1EJW 3-azanyl-7-chloranyl-4-(2-methyl-5-oxidanyl-phenyl)-1H-1,5-naphthyridin-2-one × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.1 M CALCIUM CHLORIDE, 0.05 M TRIS pH 8.5, 10 % PEG 4000
Resolution 2.17 Å R-free 0.234
9LGN Crystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 40 Deposited 2025-01-10 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 77–361（285 aa）
Not recorded A1EJU 3-azanyl-4-(7-fluoranyl-2H-indazol-4-yl)-8-methoxy-1H-1,5-naphthyridin-2-one × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.1 M CALCIUM CHLORIDE, 0.05 M TRIS pH 8.5, 10 % PEG 4000
Resolution 2.03 Å R-free 0.241
9LGN Crystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 40 Deposited 2025-01-10 Different construct Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 77–361（285 aa）
Not recorded A1EJU 3-azanyl-4-(7-fluoranyl-2H-indazol-4-yl)-8-methoxy-1H-1,5-naphthyridin-2-one × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.1 M CALCIUM CHLORIDE, 0.05 M TRIS pH 8.5, 10 % PEG 4000
Resolution 2.03 Å R-free 0.241
9LGV Crystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 11 Deposited 2025-01-10 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–362（288 aa）
Not recorded TLA L(+)-TARTARIC ACID × 2 A1EJV 3-azanyl-7-chloranyl-4-(7-fluoranyl-1H-indazol-4-yl)-1H-1,5-naphthyridin-2-one × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.1 M CALCIUM CHLORIDE, 0.05 M TRIS pH 8.5, 10 % PEG 4000
Resolution 2.04 Å R-free 0.234
9LGV Crystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 11 Deposited 2025-01-10 Different construct Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 75–362（288 aa）
Not recorded TLA L(+)-TARTARIC ACID × 1 A1EJV 3-azanyl-7-chloranyl-4-(7-fluoranyl-1H-indazol-4-yl)-1H-1,5-naphthyridin-2-one × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.1 M CALCIUM CHLORIDE, 0.05 M TRIS pH 8.5, 10 % PEG 4000
Resolution 2.04 Å R-free 0.234
9LID Crystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 27 Deposited 2025-01-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–362（288 aa）
Not recorded A1EJX 4-[7-azanyl-8-(7-fluoranyl-1H-indazol-4-yl)-6-oxidanylidene-5H-1,5-naphthyridin-3-yl]-N,N-dimethyl-benzamide × 1 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.1 M CALCIUM CHLORIDE, 0.05 M TRIS pH 8.5, 10 % PEG 4000
Resolution 2.06 Å R-free 0.231
9LID Crystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 27 Deposited 2025-01-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 75–362（288 aa）
Not recorded A1EJX 4-[7-azanyl-8-(7-fluoranyl-1H-indazol-4-yl)-6-oxidanylidene-5H-1,5-naphthyridin-3-yl]-N,N-dimethyl-benzamide × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.1 M CALCIUM CHLORIDE, 0.05 M TRIS pH 8.5, 10 % PEG 4000
Resolution 2.06 Å R-free 0.231
9M6P Discovery of a bifunctional PKMYT1-targeting PROTAC empowered by AI-generation Deposited 2025-03-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain AAA 75–362（288 aa）
Chain BBB 75–362（288 aa）
Not recorded A1EMX 2,4-dimethyl-3-[2-(2-methylpyrimidin-5-yl)-1~{H}-pyrrolo[2,3-b]pyridin-5-yl]phenol × 6 PO4 PHOSPHATE ION × 6 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；SM5-E1+30%Gly
Resolution 2.38 Å R-free 0.290

27 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PMYT1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–286； UniProt 76–361 Author chain B； PDBConstruct 1–286； UniProt 76–361

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 23es

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 23es
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2. Structure Basics 2. Structure Basics

Entry ID entry_id23es
Deposition date deposition_date2026-02-04
Structure title titleCrystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 11
Keywords keywords;STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, PROTEIN KINASE, TYROSINE- AND THREONINE-SPECIFIC KINASE, MEMBRANE-ASSOCIATED PROTEIN KINASE, TRANSFERASE ;; TRANSFERASE
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_guinier26.60 Å
Radius of gyration Rg (electron density) rg_electron25.79 Å
Forward intensity I(0) i0133210000.00
Molecular weight molecular_weight59460.0 kDa
Excluded volume excluded_volume56793 ų
Envelope volume envelope_volume96163 ų
Hydration-shell volume shell_volume30630 ų
Envelope diameter envelope_diameter85.5 Å
Shell Rg shell_rg33.34 Å
Envelope Rg envelope_rg25.80 Å
Shape Rg shape_rg25.79 Å
Total Rg total_rg26.39 Å
Total atoms total_atoms4483
Residues n_residues563
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 dmax79.2 Å
Rg (real space) rg_real26.45 Å
Rg uncertainty (real space) rg_real_error0.41 Å
I(0) (real space) i0_real1.3320e+08
I(0) uncertainty (real space) i0_real_error1.7680e+06
Rg (reciprocal space) rg_reciprocal26.50 Å
I(0) (reciprocal space) i0_reciprocal133200000.0000
Solution quality estimate total_estimate0.8397
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.9 Å
Skewness Skewness skewness0.104
Kurtosis Kurtosis kurtosis-0.665
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha39170000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.972; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; 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)

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8. Citations (1)

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9. Files and Curves (10)