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3dk3

Crystal structure of mutant ABL kinase domain in complex with small molecule fragment

Method: X-RAY DIFFRACTION Dmax: 103.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Proto-oncogene tyrosine-protein kinase ABL1

Mus musculus

UniProt P00520

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 233–514 Mutation：Y393F, L445P SX7 2-amino-5-[3-(1-ethyl-1H-pyrazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-5-yl]-N,N-dimethylbenzamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.6；292 K；1.9M AMMONIUM SULFATE, 150 mM POTASSIUM SODIUM TARTRATE, 100 Mm SODIUM CITRATE, pH 5.6, VAPOR DIFFUSION, temperature 292K Resolution 2.02 Å R-free 0.248
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 233–514 Mutation：Y393F, L445P SX7 2-amino-5-[3-(1-ethyl-1H-pyrazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-5-yl]-N,N-dimethylbenzamide × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.6；292 K；1.9M AMMONIUM SULFATE, 150 mM POTASSIUM SODIUM TARTRATE, 100 Mm SODIUM CITRATE, pH 5.6, VAPOR DIFFUSION, temperature 292K Resolution 2.02 Å R-free 0.248

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 3DK3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1ABO CRYSTAL STRUCTURE OF THE COMPLEX OF THE ABL TYROSINE KINASE SH3 DOMAIN WITH 3BP-1 SYNTHETIC PEPTIDE Deposited 1995-05-19 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 A 61–121（61 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1ABO CRYSTAL STRUCTURE OF THE COMPLEX OF THE ABL TYROSINE KINASE SH3 DOMAIN WITH 3BP-1 SYNTHETIC PEPTIDE Deposited 1995-05-19 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 B 61–121（61 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1ABO CRYSTAL STRUCTURE OF THE COMPLEX OF THE ABL TYROSINE KINASE SH3 DOMAIN WITH 3BP-1 SYNTHETIC PEPTIDE Deposited 1995-05-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 61–121（61 aa）
Chain B 61–121（61 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1ABQ CRYSTAL STRUCTURE OF THE UNLIGANDED ABL TYROSINE KINASE SH3 DOMAIN Deposited 1995-05-19 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 61–121（61 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å
1FPU CRYSTAL STRUCTURE OF ABL KINASE DOMAIN IN COMPLEX WITH A SMALL MOLECULE INHIBITOR Deposited 2000-08-31 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 229–515（287 aa） Fragment：KINASE DOMAIN
Not recorded PRC N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]AMINO]PHENYL]-3-PYRIDINECARBOXAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；PEG 4000, magnesium chloride, mes, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.40 Å R-free 0.264
1FPU CRYSTAL STRUCTURE OF ABL KINASE DOMAIN IN COMPLEX WITH A SMALL MOLECULE INHIBITOR Deposited 2000-08-31 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 229–515（287 aa） Fragment：KINASE DOMAIN
Not recorded PRC N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]AMINO]PHENYL]-3-PYRIDINECARBOXAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；PEG 4000, magnesium chloride, mes, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.40 Å R-free 0.264
1IEP CRYSTAL STRUCTURE OF THE C-ABL KINASE DOMAIN IN COMPLEX WITH STI-571. Deposited 2001-04-10 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 229–515（287 aa） Fragment：KINASE DOMAIN
Not recorded CL CHLORIDE ION × 4 STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG 4000, MAGNESIUM CHLORIDE, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.10 Å R-free 0.262
1IEP CRYSTAL STRUCTURE OF THE C-ABL KINASE DOMAIN IN COMPLEX WITH STI-571. Deposited 2001-04-10 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 229–515（287 aa） Fragment：KINASE DOMAIN
Not recorded CL CHLORIDE ION × 2 STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG 4000, MAGNESIUM CHLORIDE, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.10 Å R-free 0.262
1M52 Crystal Structure of the c-Abl Kinase domain in complex with PD173955 Deposited 2002-07-08 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 229–515（287 aa） Fragment：Kinase Domain (residues 232-503)
Not recorded P17 6-(2,6-DICHLORO-PHENYL)-8-METHYL-2-(3-METHYLSULFANYL-PHENYLAMINO)-8H-PYRIDO[2,3-D]PYRIMIDIN-7-ONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 20000, MES, isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.254
1M52 Crystal Structure of the c-Abl Kinase domain in complex with PD173955 Deposited 2002-07-08 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 229–515（287 aa） Fragment：Kinase Domain (residues 232-503)
Not recorded P17 6-(2,6-DICHLORO-PHENYL)-8-METHYL-2-(3-METHYLSULFANYL-PHENYLAMINO)-8H-PYRIDO[2,3-D]PYRIMIDIN-7-ONE × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 20000, MES, isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.254
1OPJ Structural basis for the auto-inhibition of c-Abl tyrosine kinase Deposited 2003-03-06 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 229–515（287 aa） Fragment：KINASE DOMAIN
Not recorded CL CHLORIDE ION × 1 MYR MYRISTIC ACID × 1 STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；22% PEG 4000, 100 mM MES pH 5.6, 200 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.75 Å R-free 0.242
1OPJ Structural basis for the auto-inhibition of c-Abl tyrosine kinase Deposited 2003-03-06 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 229–515（287 aa） Fragment：KINASE DOMAIN
Not recorded CL CHLORIDE ION × 1 MYR MYRISTIC ACID × 1 STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；22% PEG 4000, 100 mM MES pH 5.6, 200 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.75 Å R-free 0.242
1OPK Structural basis for the auto-inhibition of c-Abl tyrosine kinase Deposited 2003-03-06 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 27–515（489 aa） Fragment：SH3-SH2-kinase domain
Mutation：D382N MYR MYRISTIC ACID × 1 P16 6-(2,6-DICHLOROPHENYL)-2-{[3-(HYDROXYMETHYL)PHENYL]AMINO}-8-METHYLPYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；20% PEG 3350, 200 mM potassium nitrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.80 Å R-free 0.221
2QOH Crystal Structure of Abl kinase bound with PPY-A Deposited 2007-07-20 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 229–515（287 aa） Fragment：residues 228-515
Not recorded P3Y 5-[3-(2-METHOXYPHENYL)-1H-PYRROLO[2,3-B]PYRIDIN-5-YL]-N,N-DIMETHYLPYRIDINE-3-CARBOXAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；277 K；30% PEG 4K, 0.1M Tris, 0.2M sodium acetate, pH 8.5, EVAPORATION, temperature 277K
Resolution 1.95 Å R-free 0.255
2QOH Crystal Structure of Abl kinase bound with PPY-A Deposited 2007-07-20 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 229–515（287 aa） Fragment：residues 228-515
Not recorded P3Y 5-[3-(2-METHOXYPHENYL)-1H-PYRROLO[2,3-B]PYRIDIN-5-YL]-N,N-DIMETHYLPYRIDINE-3-CARBOXAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；277 K；30% PEG 4K, 0.1M Tris, 0.2M sodium acetate, pH 8.5, EVAPORATION, temperature 277K
Resolution 1.95 Å R-free 0.255
2Z60 Crystal Structure of the T315I Mutant of Abl kinase bound with PPY-A Deposited 2007-07-21 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 229–515（287 aa） Fragment：residues 228-511
Mutation：T315I P3Y 5-[3-(2-METHOXYPHENYL)-1H-PYRROLO[2,3-B]PYRIDIN-5-YL]-N,N-DIMETHYLPYRIDINE-3-CARBOXAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；277 K；30% PEG 4K, 0.1M Tris, 0.2M Sodium acetate, pH 8.5, EVAPORATION, temperature 277K
Resolution 1.95 Å R-free 0.245
3DK6 Crystal structure of mutant ABL kinase domain in complex with small molecule fragment Deposited 2008-06-24 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 233–514（282 aa）
Mutation：Y253F, L445P Non-standard monomer：Yes (specific site not provided by mmCIF) SX7 2-amino-5-[3-(1-ethyl-1H-pyrazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-5-yl]-N,N-dimethylbenzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；292 K；1.95M AMMONIUM SULFATE, 125 mM POTASSIUM SODIUM TARTRATE, 100 mM SODIUM CITRATE, pH 5.6, VAPOR DIFFUSION, temperature 292K
Resolution 2.02 Å R-free 0.246
3DK6 Crystal structure of mutant ABL kinase domain in complex with small molecule fragment Deposited 2008-06-24 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 233–514（282 aa）
Mutation：Y253F, L445P Non-standard monomer：Yes (specific site not provided by mmCIF) SX7 2-amino-5-[3-(1-ethyl-1H-pyrazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-5-yl]-N,N-dimethylbenzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；292 K；1.95M AMMONIUM SULFATE, 125 mM POTASSIUM SODIUM TARTRATE, 100 mM SODIUM CITRATE, pH 5.6, VAPOR DIFFUSION, temperature 292K
Resolution 2.02 Å R-free 0.246
3DK7 Crystal structure of mutant ABL kinase domain in complex with small molecule fragment Deposited 2008-06-24 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 233–505（273 aa）
Mutation：T315I, L445P Non-standard monomer：Yes (specific site not provided by mmCIF) SX7 2-amino-5-[3-(1-ethyl-1H-pyrazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-5-yl]-N,N-dimethylbenzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；292 K；1.9M AMMONIUM SULFATE, 150 mM POTASSIUM SODIUM TARTRATE, 100 mM SODIUM CITRATE, pH 5.6, VAPOR DIFFUSION, temperature 292K
Resolution 2.01 Å R-free 0.242
3DK7 Crystal structure of mutant ABL kinase domain in complex with small molecule fragment Deposited 2008-06-24 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 233–505（273 aa）
Mutation：T315I, L445P Non-standard monomer：Yes (specific site not provided by mmCIF) SX7 2-amino-5-[3-(1-ethyl-1H-pyrazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-5-yl]-N,N-dimethylbenzamide × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；292 K；1.9M AMMONIUM SULFATE, 150 mM POTASSIUM SODIUM TARTRATE, 100 mM SODIUM CITRATE, pH 5.6, VAPOR DIFFUSION, temperature 292K
Resolution 2.01 Å R-free 0.242
3IK3 AP24534, a Pan-BCR-ABL Inhibitor for Chronic Myeloid Leukemia, Potently Inhibits the T315I Mutant and Overcomes Mutation-Based Resistance Deposited 2009-08-05 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 229–513（285 aa）
Mutation：T315I 0LI 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzam ide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1 M Tris-HCl (pH 8.5), 30% w/v polyethylene glycol 4000, and 0.2 M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.90 Å R-free 0.258
3IK3 AP24534, a Pan-BCR-ABL Inhibitor for Chronic Myeloid Leukemia, Potently Inhibits the T315I Mutant and Overcomes Mutation-Based Resistance Deposited 2009-08-05 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 229–513（285 aa）
Mutation：T315I 0LI 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzam ide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1 M Tris-HCl (pH 8.5), 30% w/v polyethylene glycol 4000, and 0.2 M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.90 Å R-free 0.258
3K5V Structure of Abl kinase in complex with imatinib and GNF-2 Deposited 2009-10-08 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 229–515（287 aa） Fragment：Kinase domain (UNP residues 229 to 515)
Not recorded STJ 3-(6-{[4-(trifluoromethoxy)phenyl]amino}pyrimidin-4-yl)benzamide × 1 STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；0.1 M MES pH 5.6, 0.2 M MgCl2, 18 % PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.74 Å R-free 0.231
3K5V Structure of Abl kinase in complex with imatinib and GNF-2 Deposited 2009-10-08 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 229–515（287 aa） Fragment：Kinase domain (UNP residues 229 to 515)
Not recorded STJ 3-(6-{[4-(trifluoromethoxy)phenyl]amino}pyrimidin-4-yl)benzamide × 1 STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；0.1 M MES pH 5.6, 0.2 M MgCl2, 18 % PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.74 Å R-free 0.231
3KF4 Structural analysis of DFG-in and DFG-out dual Src-Abl inhibitors sharing a common vinyl purine template Deposited 2009-10-27 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 229–515（287 aa） Fragment：residues 115-401
Not recorded B90 N-[4-(dimethylphosphoryl)phenyl]-9-[(E)-2-(5-methyl-1H-indazol-4-yl)ethenyl]-9H-purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1 M TRIS-HCL, pH 8.0, 30% w/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.90 Å R-free 0.240
3KF4 Structural analysis of DFG-in and DFG-out dual Src-Abl inhibitors sharing a common vinyl purine template Deposited 2009-10-27 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 229–515（287 aa） Fragment：residues 115-401
Not recorded B90 N-[4-(dimethylphosphoryl)phenyl]-9-[(E)-2-(5-methyl-1H-indazol-4-yl)ethenyl]-9H-purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1 M TRIS-HCL, pH 8.0, 30% w/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.90 Å R-free 0.240
3KFA Structural analysis of DFG-in and DFG-out dual Src-Abl inhibitors sharing a common vinyl purine template Deposited 2009-10-27 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 229–515（287 aa） Fragment：residues 115-401
Not recorded B91 3-{(E)-2-[6-(cyclopropylamino)-9H-purin-9-yl]ethenyl}-4-methyl-N-[3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1 M TRIS-HCL, pH 8.5, 30% w/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.22 Å R-free 0.201
3KFA Structural analysis of DFG-in and DFG-out dual Src-Abl inhibitors sharing a common vinyl purine template Deposited 2009-10-27 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 229–515（287 aa） Fragment：residues 115-401
Not recorded B91 3-{(E)-2-[6-(cyclopropylamino)-9H-purin-9-yl]ethenyl}-4-methyl-N-[3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1 M TRIS-HCL, pH 8.5, 30% w/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.22 Å R-free 0.201
3MS9 ABL kinase in complex with imatinib and a fragment (FRAG1) in the myristate pocket Deposited 2010-04-29 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 229–515（287 aa） Fragment：KINASE DOMAIN, residues 229-515
Not recorded STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 1 MS9 methyl 2-amino-4-chlorobenzoate × 1 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；protein concentration: 20mg/ml. Crystallisation buffer: 0.1M MES pH 6.5, 0.2M MgCl2, 18.4% PEG4000, VAPOR DIFFUSION, temperature 277K
Resolution 1.80 Å R-free 0.234
3MS9 ABL kinase in complex with imatinib and a fragment (FRAG1) in the myristate pocket Deposited 2010-04-29 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 B 229–515（287 aa） Fragment：KINASE DOMAIN, residues 229-515
Not recorded STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 1 MS9 methyl 2-amino-4-chlorobenzoate × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；protein concentration: 20mg/ml. Crystallisation buffer: 0.1M MES pH 6.5, 0.2M MgCl2, 18.4% PEG4000, VAPOR DIFFUSION, temperature 277K
Resolution 1.80 Å R-free 0.234
3MSS Abl kinase in complex with imatinib and fragment (FRAG2) in the myristate site Deposited 2010-04-29 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 229–515（287 aa） Fragment：KINASE DOMAIN, residues 229-515
Not recorded STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 1 MS7 O-benzyl-N-methyl-L-tyrosinamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；Buffer: 0.1M imidazole pH 6.5, 0.2M MgCl2, 2%EG, 13.8% PEG4000, VAPOR DIFFUSION, temperature 277K
Resolution 1.95 Å R-free 0.220
3MSS Abl kinase in complex with imatinib and fragment (FRAG2) in the myristate site Deposited 2010-04-29 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 B 229–515（287 aa） Fragment：KINASE DOMAIN, residues 229-515
Not recorded STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 1 MS7 O-benzyl-N-methyl-L-tyrosinamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；Buffer: 0.1M imidazole pH 6.5, 0.2M MgCl2, 2%EG, 13.8% PEG4000, VAPOR DIFFUSION, temperature 277K
Resolution 1.95 Å R-free 0.220
3MSS Abl kinase in complex with imatinib and fragment (FRAG2) in the myristate site Deposited 2010-04-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 229–515（287 aa） Fragment：KINASE DOMAIN, residues 229-515
Not recorded STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 1 MS7 O-benzyl-N-methyl-L-tyrosinamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；Buffer: 0.1M imidazole pH 6.5, 0.2M MgCl2, 2%EG, 13.8% PEG4000, VAPOR DIFFUSION, temperature 277K
Resolution 1.95 Å R-free 0.220
3MSS Abl kinase in complex with imatinib and fragment (FRAG2) in the myristate site Deposited 2010-04-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 229–515（287 aa） Fragment：KINASE DOMAIN, residues 229-515
Not recorded STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 1 MS7 O-benzyl-N-methyl-L-tyrosinamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；Buffer: 0.1M imidazole pH 6.5, 0.2M MgCl2, 2%EG, 13.8% PEG4000, VAPOR DIFFUSION, temperature 277K
Resolution 1.95 Å R-free 0.220
3OXZ Crystal structure of ABL kinase domain bound with a DFG-out inhibitor AP24534 Deposited 2010-09-22 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 229–511（283 aa） Fragment：UNP residues 229-511
Not recorded 0LI 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzam ide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；30% w/v polyethylene glycol, 0.2 M sodium acetate, 0.1 M Tris-HCl, pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.261
3OY3 Crystal structure of ABL T315I mutant kinase domain bound with a DFG-out inhibitor AP24589 Deposited 2010-09-22 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 229–511（283 aa） Fragment：UNP residues 229-511
Mutation：T315I XY3 5-[(5-{[4-{[4-(2-hydroxyethyl)piperazin-1-yl]methyl}-3-(trifluoromethyl)phenyl]carbamoyl}-2-methylphenyl)ethynyl]-1-methyl-1H-imidazole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；30% w/v polyethylene glycol, 0.2 M sodium acetate, 0.1 M Trs-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.266
3OY3 Crystal structure of ABL T315I mutant kinase domain bound with a DFG-out inhibitor AP24589 Deposited 2010-09-22 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 229–511（283 aa） Fragment：UNP residues 229-511
Mutation：T315I XY3 5-[(5-{[4-{[4-(2-hydroxyethyl)piperazin-1-yl]methyl}-3-(trifluoromethyl)phenyl]carbamoyl}-2-methylphenyl)ethynyl]-1-methyl-1H-imidazole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；30% w/v polyethylene glycol, 0.2 M sodium acetate, 0.1 M Trs-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.266
6HD4 ABL1 IN COMPLEX WITH COMPOUND 7 AND IMATINIB (STI-571) Deposited 2018-08-17 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 229–515（287 aa） Fragment：KINASE DOMAIN
Not recorded GOL GLYCEROL × 1 CL CHLORIDE ION × 1 FYW 6-[(3~{R})-3-oxidanylpyrrolidin-1-yl]-5-pyrimidin-5-yl-~{N}-[4-(trifluoromethyloxy)phenyl]pyridine-3-carboxamide × 1 STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；20.0 % PEG 4000, 0.2 M MGCL2, 0.1 M MES PH 5.6
Resolution 2.03 Å R-free 0.223
6HD4 ABL1 IN COMPLEX WITH COMPOUND 7 AND IMATINIB (STI-571) Deposited 2018-08-17 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 229–515（287 aa） Fragment：KINASE DOMAIN
Not recorded FYW 6-[(3~{R})-3-oxidanylpyrrolidin-1-yl]-5-pyrimidin-5-yl-~{N}-[4-(trifluoromethyloxy)phenyl]pyridine-3-carboxamide × 1 STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；20.0 % PEG 4000, 0.2 M MGCL2, 0.1 M MES PH 5.6
Resolution 2.03 Å R-free 0.223
6HD6 ABL1 IN COMPLEX WITH COMPOUND6 AND IMATINIB (STI-571) Deposited 2018-08-17 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 229–515（287 aa） Fragment：KINASE DOMAIN
Not recorded CL CHLORIDE ION × 1 FYH 3-(morpholin-4-ylmethyl)-~{N}-[4-(trifluoromethyloxy)phenyl]benzamide × 1 STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；21.4 % PEG 4000, 0.2 M MGCL2, 0.1 M MES PH 5.6
Resolution 2.30 Å R-free 0.238
6HD6 ABL1 IN COMPLEX WITH COMPOUND6 AND IMATINIB (STI-571) Deposited 2018-08-17 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 229–515（287 aa） Fragment：KINASE DOMAIN
Not recorded STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；21.4 % PEG 4000, 0.2 M MGCL2, 0.1 M MES PH 5.6
Resolution 2.30 Å R-free 0.238

21 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ABL1_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–285； UniProt 233–514 Author chain B； PDBConstruct 4–285； UniProt 233–514

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 3dk3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3dk3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3dk3
Deposition date deposition_date2008-06-24
Structure title titleCrystal structure of mutant ABL kinase domain in complex with small molecule fragment
Keywords keywords;DRUG DISCOVERY, ABL KINASE, FRAGMENT BASED, Alternative splicing, ATP-binding, Cell adhesion, Chromosomal rearrangement, Cytoplasm, Cytoskeleton, Kinase, Lipoprotein, Magnesium, Manganese, Metal-binding, Myristate, Nucleotide-binding, Nucleus, Phosphoprotein, Proto-oncogene, SH2 domain, SH3 domain, 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_guinier31.24 Å
Radius of gyration Rg (electron density) rg_electron31.20 Å
Forward intensity I(0) i057685400.00
Molecular weight molecular_weight61537.0 kDa
Excluded volume excluded_volume77527 ų
Envelope volume envelope_volume100240 ų
Hydration-shell volume shell_volume27933 ų
Envelope diameter envelope_diameter108.1 Å
Shell Rg shell_rg36.71 Å
Envelope Rg envelope_rg30.95 Å
Shape Rg shape_rg31.18 Å
Total Rg total_rg31.79 Å
Total atoms total_atoms4333
Residues n_residues535
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 dmax103.8 Å
Rg (real space) rg_real31.47 Å
Rg uncertainty (real space) rg_real_error0.79 Å
I(0) (real space) i0_real5.7690e+07
I(0) uncertainty (real space) i0_real_error9.4680e+05
Rg (reciprocal space) rg_reciprocal31.38 Å
I(0) (reciprocal space) i0_reciprocal57680000.0000
Solution quality estimate total_estimate0.8321
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary26.4 Å
Skewness Skewness skewness0.418
Kurtosis Kurtosis kurtosis-0.590
Angular range angular_range— – 0.2550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17700000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.783; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.665; Smooth: 0.799
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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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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3dk3a_
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.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd3dk3b_
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.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (4 domains)

Domain ID domain_id3dk3A01
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_id3dk3A02
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_id3dk3B01
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_id3dk3B02
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)