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4qo9

MST3 IN COMPLEX WITH Danusertib

Method: X-RAY DIFFRACTION Dmax: 90.9 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SERINE/THREONINE-PROTEIN KINASE 24

Homo sapiens

UniProt Q9Y6E0

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 1–303 Fragment：RESIDUES 1-303 Mutation：NO Non-standard monomer：Yes (specific site not provided by mmCIF) PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1 627 N-[(3E)-5-[(2R)-2-METHOXY-2-PHENYLACETYL]PYRROLO[3,4-C]PYRAZOL-3(5H)-YLIDENE]-4-(4-METHYLPIPERAZIN-1-YL)BENZAMIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 mg/mL MST3, 1 mM Danusertib, 25 mM TRIS, PH 8.0, 50 MM HEPES pH 7.5, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.20 Å R-free 0.218
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–303 Fragment：RESIDUES 1-303 Mutation：NO Non-standard monomer：Yes (specific site not provided by mmCIF) PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 1 627 N-[(3E)-5-[(2R)-2-METHOXY-2-PHENYLACETYL]PYRROLO[3,4-C]PYRAZOL-3(5H)-YLIDENE]-4-(4-METHYLPIPERAZIN-1-YL)BENZAMIDE × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 mg/mL MST3, 1 mM Danusertib, 25 mM TRIS, PH 8.0, 50 MM HEPES pH 7.5, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.20 Å R-free 0.218
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–303 Chain B； UniProt 1–303 Fragment：RESIDUES 1-303 Mutation：NO Non-standard monomer：Yes (specific site not provided by mmCIF) PGE TRIETHYLENE GLYCOL × 2 EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 1 627 N-[(3E)-5-[(2R)-2-METHOXY-2-PHENYLACETYL]PYRROLO[3,4-C]PYRAZOL-3(5H)-YLIDENE]-4-(4-METHYLPIPERAZIN-1-YL)BENZAMIDE × 2 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 mg/mL MST3, 1 mM Danusertib, 25 mM TRIS, PH 8.0, 50 MM HEPES pH 7.5, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.20 Å R-free 0.218

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 4QO9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3CKW Crystal structure of sterile 20-like kinase 3 (MST3, STK24) Deposited 2008-03-17 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 31–323（293 aa）
Not recorded HG MERCURY (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；292 K；22% PEG 4000, 100 mM Tris-HCl, 200 mM Sodium acetate, pH 8.5, VAPOR DIFFUSION, temperature 292K
Resolution 1.96 Å R-free 0.265
3CKX Crystal structure of sterile 20-like kinase 3 (MST3, STK24) in complex with staurosporine Deposited 2008-03-17 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 31–323（293 aa） Fragment：Residues 31-323
Non-standard monomer：Yes (specific site not provided by mmCIF) STU STAUROSPORINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；292 K；22% PEG 4000, 100 mM Tris-HCl, 200 mM Sodium acetate, pH 8.5, VAPOR DIFFUSION, temperature 292K
Resolution 2.70 Å R-free 0.268
3ZHP Human MST3 (STK24) in complex with MO25beta Deposited 2012-12-24 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 D 19–289（271 aa） Fragment：KINASE DOMAIN, RESIDUES 19-289
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.2M NA/KPO4, 10% PEG 3350, 10% ETHYLENE GLYCOL, pH 7.5
Resolution 2.90 Å R-free 0.261
3ZHP Human MST3 (STK24) in complex with MO25beta Deposited 2012-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 19–289（271 aa） Fragment：KINASE DOMAIN, RESIDUES 19-289
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.2M NA/KPO4, 10% PEG 3350, 10% ETHYLENE GLYCOL, pH 7.5
Resolution 2.90 Å R-free 0.261
4O27 Crystal structure of MST3-MO25 complex with WIF motif Deposited 2013-12-16 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 B 30–309（280 aa） Fragment：Kinase domain, UNP residues 30-309
Chain C 336–340（5 aa） Fragment：WIF motif, UNP residues 336-340
Mutation：T190E Mutation：T340E ADP ADENOSINE-5'-DIPHOSPHATE × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；0.1M Tris pH 8.5, 2.0M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 3.19 Å R-free 0.260
4QML MST3 in complex with AMP-PNP Deposited 2014-06-16 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 1–303（303 aa） Fragment：unp residues 1-303
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 mg/mL MST3, 1 mM ANP-PNP, 25 mM TRIS, PH 8.0, 50 MM HEPES pH 7.5, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.88 Å R-free 0.230
4QMM MST3 IN COMPLEX WITH AT-9283, 4-[(2-{4-[(CYCLOPROPYLCARBAMOYL)AMINO]-1H-PYRAZOL-3-YL}-1H-BENZIMIDAZOL-6-YL)METHYL]MORPHOLIN-4-IUM Deposited 2014-06-16 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 1–303（303 aa） Fragment：unp residues 1-303
Non-standard monomer：Yes (specific site not provided by mmCIF) 35R 1-cyclopropyl-3-{3-[5-(morpholin-4-ylmethyl)-1H-benzimidazol-2-yl]-1H-pyrazol-4-yl}urea × 1 ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 mg/mL MST3, 1 mM AT-9283, 25 mM TRIS, 50 MM HEPES pH 7.5, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.85 Å R-free 0.198
4QMN MST3 in complex with BOSUTINIB Deposited 2014-06-16 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 27–315（289 aa） Fragment：unp residues 1-303
Non-standard monomer：Yes (specific site not provided by mmCIF) DB8 4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 mg/mL MST3, 1 mM BOSUTINIB, 25 mM TRIS, PH 8.0, 50 MM HEPES, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.09 Å R-free 0.227
4QMO MST3 IN COMPLEX WITH Imidazolo-oxindole PKR inhibitor C16 Deposited 2014-06-16 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 1–303（303 aa） Fragment：RESIDUES 1-303
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 34L (8Z)-8-(1H-imidazol-5-ylmethylidene)-6,8-dihydro-7H-[1,3]thiazolo[5,4-e]indol-7-one × 1 PG4 TETRAETHYLENE GLYCOL × 1 DMS DIMETHYL SULFOXIDE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 mg/mL MST3, 1 mM C16, 25 mM TRIS, PH 8.0, 50 MM HEPES pH 7.5, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.90 Å R-free 0.204
4QMP MST3 IN COMPLEX WITH CDK1/2 INHIBITOR III, 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE Deposited 2014-06-16 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 1–303（303 aa） Fragment：RESIDUES 1-303
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 DKI 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；291 K；12.5 mg/mL MST3, 1 mM CDK2 Inhibitor III, 25 mM TRIS, PH 8.0, 50 MM HEPES pH 7.5, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.00 Å R-free 0.228
4QMQ MST3 in complex with CP-673451 Deposited 2014-06-16 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 1–303（303 aa） Fragment：unp residues 1-303
Non-standard monomer：Yes (specific site not provided by mmCIF) 34U 1-{2-[5-(2-methoxyethoxy)-1H-benzimidazol-1-yl]quinolin-8-yl}piperidin-4-amine × 1 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 mg/mL MST3, 1 mM CP-673451, 25 mM TRIS, PH 8.0, 50 MM HEPES pH 7.5, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.77 Å R-free 0.215
4QMS MST3 in complex with DASATINIB Deposited 2014-06-16 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 1–303（303 aa） Fragment：unp residues 1-303
Non-standard monomer：Yes (specific site not provided by mmCIF) 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 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 mg/mL MST3, 1 mM DASATINIB, 25 mM TRIS, PH 8.0, 50 MM HEPES pH 7.5, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.88 Å R-free 0.214
4QMT MST3 in complex with HESPERADIN Deposited 2014-06-16 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 1–303（303 aa） Fragment：unp residues 1-303
Non-standard monomer：Yes (specific site not provided by mmCIF) H1N N-[2-OXO-3-((E)-PHENYL{[4-(PIPERIDIN-1-YLMETHYL)PHENYL]IMINO}METHYL)-2,6-DIHYDRO-1H-INDOL-5-YL]ETHANESULFONAMIDE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 mg/mL MST3, 1 mM HESPERADIN, 25 mM TRIS, PH 8.0, 50 MM HEPES pH 7.5, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.50 Å R-free 0.185
4QMU MST3 IN COMPLEX WITH JNJ-7706621, 4-({5-AMINO-1-[(2,6-DIFLUOROPHENYL)CARBONYL]-1H-1,2,4-TRIAZOL-3-YL}AMINO)BENZENESULFONAMIDE Deposited 2014-06-16 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 1–303（303 aa） Fragment：unp residues 1-303
Non-standard monomer：Yes (specific site not provided by mmCIF) SKE 4-({5-amino-1-[(2,6-difluorophenyl)carbonyl]-1H-1,2,4-triazol-3-yl}amino)benzenesulfonamide × 1 MG MAGNESIUM ION × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 mg/mL MST3, 1 mM JNJ-7706621, 25 mM TRIS, PH 8.0, 50 MM HEPES pH 7.5, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.55 Å R-free 0.206
4QMV MST3 IN COMPLEX WITH PF-03814735, 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 Deposited 2014-06-16 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 1–303（303 aa） Fragment：RESIDUES 1-303
Non-standard monomer：Yes (specific site not provided by mmCIF) 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 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 mg/mL MST3, 1 mM PF-03814735, 25 mM TRIS, PH 8.0, 50 MM HEPES pH 7.5, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.40 Å R-free 0.226
4QMW MST3 IN COMPLEX WITH PP-121, 1-CYCLOPENTYL-3-(1H-PYRROLO[2,3-B]PYRIDIN-5-YL)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-AMINE Deposited 2014-06-16 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 1–303（303 aa） Fragment：unp residues 1-303
Non-standard monomer：Yes (specific site not provided by mmCIF) KS1 1-cyclopentyl-3-(1H-pyrrolo[2,3-b]pyridin-5-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine × 1 EDO 1,2-ETHANEDIOL × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 mg/mL MST3, 1 mM PP-121, 25 mM TRIS, PH 8.0, 50 MM HEPES pH 7.5, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.60 Å R-free 0.211
4QMX MST3 in complex with SARACATINIB Deposited 2014-06-16 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 1–303（303 aa） Fragment：unp residues 1-303
Non-standard monomer：Yes (specific site not provided by mmCIF) 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 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 mg/mL MST3, 1 mM SARACATINIB,25 mM TRIS, PH 8.0, 50 MM HEPES pH 7.5, 125 mM SODIUM, CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.88 Å R-free 0.218
4QMY MST3 IN COMPLEX WITH STAUROSPORINE Deposited 2014-06-16 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 1–303（303 aa） Fragment：unp residues 1-303
Non-standard monomer：Yes (specific site not provided by mmCIF) STU STAUROSPORINE × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 mg/mL MST3, 1 mM STAUROSPORINE, 25 mM TRIS, PH 8.0, 50 MM HEPES pH 7.5, 125 mM SODIUM, CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.88 Å R-free 0.220
4QMZ MST3 IN COMPLEX WITH SUNITINIB Deposited 2014-06-16 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 1–303（303 aa） Fragment：unp residues 1-303
Non-standard monomer：Yes (specific site not provided by mmCIF) B49 N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carbo xamide × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 mg/mL MST3, 1 mM SUNITINIB, 25 mM TRIS, PH 8.0, 50 MM HEPES, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.88 Å R-free 0.224
4U8Z Crystal structure of MST3 with a pyrrolopyrimidine inhibitor (PF-06447475) Deposited 2014-08-05 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 9–298（290 aa） Fragment：UNP residues 9-298
Non-standard monomer：Yes (specific site not provided by mmCIF) MN MANGANESE (II) ION × 1 3FE 3-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]benzonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M Tris-HCl (pH 8.5), 180mM MgCl2, 5mM Manganese (II) acetate, 10-17% PEG3350
Resolution 1.63 Å R-free 0.222
4W8D Crystal structure of MST3 with a pyrrolopyrimidine inhibitor (PF-06454589). Deposited 2014-08-24 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 9–298（290 aa） Fragment：UNP residues 9-298
Non-standard monomer：Yes (specific site not provided by mmCIF) 3JA 5-(1-methyl-1H-pyrazol-4-yl)-4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M Tris-HCL (pH 8.5), 180mM MgCl2, 5mM Manganese acetate, 10-17% PEG 3350
Resolution 1.77 Å R-free 0.182
4W8E Structure of MST3 with a pyrrolopyrimidine inhibitor (PF-06645342) Deposited 2014-08-24 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 9–299（291 aa） Fragment：UNP residues 9-298
Non-standard monomer：Yes (specific site not provided by mmCIF) 3JB 3-{4-[(2R)-2-(5-methyl-1,2,4-oxadiazol-3-yl)morpholin-4-yl]-7H-pyrrolo[2,3-d]pyrimidin-5-yl}benzonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M Tris-HCl (pH 8.5), 180mM MgCl2, 5mM Manganese acetate, 10-17% PEG3350
Resolution 1.79 Å R-free 0.212
7B30 MST3 in complex with compound G-5555 Deposited 2020-11-28 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 4–301（298 aa）
Not recorded 59T 8-[(trans-5-amino-1,3-dioxan-2-yl)methyl]-6-[2-chloro-4-(6-methylpyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 10 mg/ml in buffer 25 mM HEPES pH 7.5, 200 mM NaCl, 5% glycerol and 0.5 mM TCEP. Reservoir: 10% PEG 6000, 0.1M HEPES pH 7.0.
Resolution 2.10 Å R-free 0.196
7B31 MST3 in complex with compound MRIA9 Deposited 2020-11-28 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 4–301（298 aa）
Not recorded SQ8 1-[(5-azanyl-1,3-dioxan-2-yl)methyl]-3-[2-chloranyl-4-(3-fluoranylpyridin-2-yl)phenyl]-7-(methylamino)-1,6-naphthyridin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 10 mg/ml in buffer 25 mM HEPES pH 7.5, 200 mM NaCl, 5% glycerol, 0.5 mM TCEP. Reservoir: 16% PEG 6000, 0.1M HEPES pH 7.0.
Resolution 1.80 Å R-free 0.212
7B32 MST3 in complex with MRIA7 Deposited 2020-11-28 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 4–301（298 aa）
Not recorded SQQ 8-[(5-azanyl-1,3-dioxan-2-yl)methyl]-6-[2-chloranyl-4-(6-methylpyridin-2-yl)phenyl]-2-[(2-methoxyphenyl)amino]pyrido[2,3-d]pyrimidin-7-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 10 mg/ml in buffer 25 mM HEPES pH 7.5, 200 mM NaCl, 5% glycerol, 0.5mM TCEP. Reservoir: 20% PEG 3350, 0.1M bis-tris pH 6.5.
Resolution 1.75 Å R-free 0.203
7B33 MST3 in complex with MRIA11 Deposited 2020-11-28 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 4–301（298 aa）
Not recorded EDO 1,2-ETHANEDIOL × 4 SQE 8-[(5-azanyl-1,3-dioxan-2-yl)methyl]-6-[4-[6-[bis(fluoranyl)methyl]pyridin-2-yl]-2-chloranyl-phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 10 mg/ml in buffer 25 mM HEPES pH 7.5, 200 mM NaCl, 5% glycerol, 0.5 mM TCEP. Reservoir: 19% PEG 3350, 0.1M bis-tris pH 6.8.
Resolution 1.90 Å R-free 0.208
7B34 MST3 in complex with compound MRIA12 Deposited 2020-11-28 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 4–301（298 aa）
Not recorded EDO 1,2-ETHANEDIOL × 7 SQK 8-[(5-azanyl-1,3-dioxan-2-yl)methyl]-6-[2-chloranyl-4-(3-fluoranyl-6-methyl-pyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 10 mg/ml in buffer 25 mM HEPES pH 7.5, 200 mM NaCl, 5% glycerol, 0.5 mM TCEP. Reservoir: 14% PEG 6000, 0.1M HEPES pH 7.2.
Resolution 2.10 Å R-free 0.215
7B35 MST3 in complex with compound MRIA13 Deposited 2020-11-28 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 4–301（298 aa）
Not recorded SQB 8-[(5-azanyl-1,3-dioxan-2-yl)methyl]-6-[2-chloranyl-4-(3-methoxy-6-methyl-pyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 10 mg/ml in buffer 25 mM HEPES pH 7.5, 200 mM NaCl, 5% glycerol, 0.5 mM TCEP. reservoir: 24% PEG 3550, 0.1M citrate pH 5.6.
Resolution 2.40 Å R-free 0.263
7B35 MST3 in complex with compound MRIA13 Deposited 2020-11-28 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 B 4–301（298 aa）
Not recorded SQB 8-[(5-azanyl-1,3-dioxan-2-yl)methyl]-6-[2-chloranyl-4-(3-methoxy-6-methyl-pyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 10 mg/ml in buffer 25 mM HEPES pH 7.5, 200 mM NaCl, 5% glycerol, 0.5 mM TCEP. reservoir: 24% PEG 3550, 0.1M citrate pH 5.6.
Resolution 2.40 Å R-free 0.263
8BZI Human MST3 (STK24) kinase in complex with inhibitor MR39 Deposited 2022-12-14 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 4–301（298 aa）
Not recorded SJL 8-(4-azanylbutyl)-6-[2,5-bis(fluoranyl)-4-(6-methylpyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7-one × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 11 mg/mL MST3 in 25 mM HEPES pH 7.5, 200 mM NaCl, 0.5 mM TCEP, 5% glycerol, with 1 mM inhibitor). Crystallization buffer: 20% PEG 3350, 0.1 M bis-tris pH 6.5.
Resolution 1.72 Å R-free 0.196
8BZJ Human MST3 (STK24) kinase in complex with inhibitor MRLW5 Deposited 2022-12-14 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 4–301（298 aa）
Not recorded SJX 8-(4-azanylbutyl)-6-[2-chloranyl-4-(6-methylpyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 11 mg/mL MST3 in 25 mM HEPES pH 7.5, 200 mM NaCl, 0.5 mM TCEP, 5% glycerol, with 1 mM inhibitor). Crystallization buffer: 12% PEG 6000, 0.1 M HEPES pH 7.4.
Resolution 2.52 Å R-free 0.250
8BZJ Human MST3 (STK24) kinase in complex with inhibitor MRLW5 Deposited 2022-12-14 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 B 4–301（298 aa）
Not recorded SJX 8-(4-azanylbutyl)-6-[2-chloranyl-4-(6-methylpyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7-one × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 11 mg/mL MST3 in 25 mM HEPES pH 7.5, 200 mM NaCl, 0.5 mM TCEP, 5% glycerol, with 1 mM inhibitor). Crystallization buffer: 12% PEG 6000, 0.1 M HEPES pH 7.4.
Resolution 2.52 Å R-free 0.250
8QLQ Human MST3 (STK24) kinase in complex with macrocyclic inhibitor JA310 Deposited 2023-09-20 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 4–301（298 aa）
Not recorded VY0 macrocyclic inhibitor × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 11 mg/mL MST3 in 25 mM HEPES pH 7.5, 200 mM NaCl, 0.5 mM TCEP, 5% glycerol) with 3 mM macrocyclic inhibitor JA310. Reservoir solution: 14% PEG 6K, 0.1 M HEPES pH 7.2. Drop ratio 1:2.
Resolution 1.64 Å R-free 0.227
8QLR Human MST3 (STK24) kinase in complex with inhibitor MR24 Deposited 2023-09-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 4–301（298 aa）
Chain B 4–301（298 aa）
Not recorded VYN 8-(4-azanylbutyl)-2-[1,3-bis(oxidanyl)propan-2-ylamino]-6-[2-chloranyl-4-(6-methylpyridin-2-yl)phenyl]pyrido[2,3-d]pyrimidin-7-one × 2 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 11 mg/mL MST3 in 25 mM HEPES pH 7.5, 200 mM NaCl, 0.5 mM TCEP, 5% glycerol) with 1 mM compound MR24. Reservoir solution: 28% PEG 3350, 0.1 M citrate pH 5.6
Resolution 1.85 Å R-free 0.217
8QLS Human MST3 (STK24) kinase in complex with inhibitor MR26 Deposited 2023-09-20 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 4–301（298 aa）
Not recorded VYH 8-(4-azanylbutyl)-6-[2-chloranyl-4-(6-methylpyridin-2-yl)phenyl]-2-(3-morpholin-4-ylpropylamino)pyrido[2,3-d]pyrimidin-7-one × 1 EDO 1,2-ETHANEDIOL × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 11 mg/mL MST3 in 25 mM HEPES pH 7.5, 200 mM NaCl, 0.5 mM TCEP, 5% glycerol) with 1 mM compound MR26. Reservoir solution: 10% PEG 6000, 0.1 M HEPES pH 7.2
Resolution 1.61 Å R-free 0.184
8QLT Human MST3 (STK24) kinase in complex with inhibitor MR30 Deposited 2023-09-20 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 4–301（298 aa）
Not recorded VZ2 8-(4-azanylbutyl)-6-[2-chloranyl-4-(6-methylpyridin-2-yl)phenyl]-2-[3-(2-oxidanylidenepyrrolidin-1-yl)propylamino]pyrido[2,3-d]pyrimidin-7-one × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein solution: 11 mg/mL MST3 in 25 mM HEPES pH 7.5, 200 mM NaCl, 0.5 mM TCEP, 5% glycerol) with 1 mM compound MR30. Reservoir solution: 24% PEG 3350, 0.1M citrate pH 5.2
Resolution 1.47 Å R-free 0.176

33 other PDB entries and 36 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name STK24_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–310； UniProt 1–303 Author chain B； PDBConstruct 8–310； UniProt 1–303

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 4qo9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4qo9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4qo9
Deposition date deposition_date2014-06-19
Structure title titleMST3 IN COMPLEX WITH Danusertib
Keywords keywords;PROTEIN KINASE, MST3, STK24, STERILE 20-LIKE KINASE, ATP-BINDING, NUCLEOTIDE-BINDING, PHOSPHOPROTEIN, SERINE/THREONINE-TRANSFERASE, Transferase-transferase inhibitor complex ;; Transferase/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_guinier28.18 Å
Radius of gyration Rg (electron density) rg_electron27.25 Å
Forward intensity I(0) i065594500.00
Molecular weight molecular_weight66000.0 kDa
Excluded volume excluded_volume83859 ų
Envelope volume envelope_volume102950 ų
Hydration-shell volume shell_volume31717 ų
Envelope diameter envelope_diameter93.7 Å
Shell Rg shell_rg34.46 Å
Envelope Rg envelope_rg27.25 Å
Shape Rg shape_rg27.23 Å
Total Rg total_rg28.10 Å
Total atoms total_atoms4653
Residues n_residues565
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 dmax90.9 Å
Rg (real space) rg_real28.15 Å
Rg uncertainty (real space) rg_real_error0.45 Å
I(0) (real space) i0_real6.5590e+07
I(0) uncertainty (real space) i0_real_error8.3880e+05
Rg (reciprocal space) rg_reciprocal28.16 Å
I(0) (reciprocal space) i0_reciprocal65590000.0000
Solution quality estimate total_estimate0.9014
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.8 Å
Skewness Skewness skewness0.297
Kurtosis Kurtosis kurtosis-0.517
Angular range angular_range— – 0.2800 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha13910000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.985
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4qo9a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.0 — automated matches
Domain ID domain_idd4qo9b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id4qo9A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id4qo9A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id4qo9B01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id4qo9B02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
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8. Citations (1)

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9. Files and Curves (10)