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1u4d

Structure of the ACK1 Kinase Domain bound to Debromohymenialdisine

Method: X-RAY DIFFRACTION Dmax: 82.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Activated CDC42 kinase 1

Homo sapiens

UniProt Q07912

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 10–296 Fragment：Kinase Domain DBQ DEBROMOHYMENIALDISINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；291 K；PEG 2000, sodium chloride, magnesium chloride, TRIS, TCEP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 7.50 Resolution 2.10 Å R-free 0.248
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 10–296 Fragment：Kinase Domain DBQ DEBROMOHYMENIALDISINE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；291 K；PEG 2000, sodium chloride, magnesium chloride, TRIS, TCEP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 7.50 Resolution 2.10 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 1U4D Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CF4 CDC42/ACK GTPASE-BINDING DOMAIN COMPLEX Deposited 1999-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 446–489（44 aa） Fragment：GTPASE-BINDING DOMAIN
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 SOLUTION NMR
NMR measurement conditions pH 5.5；298 K
NMR sample composition [50%2H; 100%15N,13C]-labelled Cdc42, unlabelled f-ACK, 90% H2O/10% | 90% H2O/10% D2O
NMR sample composition [U-15N] f-ACK, Cdc42, 90% H2O/10% | 90% H2O/10% D2O
NMR sample composition [U-13C; U-15N] f-ACK, Cdc42, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition [U-13C; U-15N] Cdc42, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition [U-100% 15N] Cdc42, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
1U46 Crystal Structure of the Unphosphorylated Kinase Domain of the Tyrosine Kinase ACK1 Deposited 2004-07-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 109–395（287 aa） Fragment：Kinase Domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；PEG 4000, magnesium chloride, sodium chloride, HEPES, TRIS, TCEP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.00 Å R-free 0.249
1U46 Crystal Structure of the Unphosphorylated Kinase Domain of the Tyrosine Kinase ACK1 Deposited 2004-07-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 109–395（287 aa） Fragment：Kinase Domain
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；PEG 4000, magnesium chloride, sodium chloride, HEPES, TRIS, TCEP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.00 Å R-free 0.249
1U54 Crystal Structures of the Phosphorylated and Unphosphorylated Kinase Domains of the CDC42-associated Tyrosine Kinase ACK1 bound to AMP-PCP Deposited 2004-07-26 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 109–395（287 aa） Fragment：Kinase Domain
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；291 K；PEG 4000, lithium sulfate, magnesium chloride, sodium chloride, AMP-PCP, Tris, TCEP, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 8.50
Resolution 2.80 Å R-free 0.322
1U54 Crystal Structures of the Phosphorylated and Unphosphorylated Kinase Domains of the CDC42-associated Tyrosine Kinase ACK1 bound to AMP-PCP Deposited 2004-07-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 109–395（287 aa） Fragment：Kinase Domain
Not recorded MG MAGNESIUM ION × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；291 K；PEG 4000, lithium sulfate, magnesium chloride, sodium chloride, AMP-PCP, Tris, TCEP, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 8.50
Resolution 2.80 Å R-free 0.322
3EQP Crystal Structure of Ack1 with compound T95 Deposited 2008-10-01 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 117–392（276 aa） Fragment：UNP residues 117-392
Chain B 117–392（276 aa） Fragment：UNP residues 117-392
Not recorded T95 N-(2,6-dimethylphenyl)-4-(2-ethoxyphenoxy)-2-({4-[4-(2-hydroxyethyl)piperazin-1-yl]phenyl}amino)pyrimidine-5-carboxamide × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；vapor diffusion, temperature 298K
Resolution 2.30 Å R-free 0.284
3EQP Crystal Structure of Ack1 with compound T95 Deposited 2008-10-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 117–392（276 aa） Fragment：UNP residues 117-392
Not recorded T95 N-(2,6-dimethylphenyl)-4-(2-ethoxyphenoxy)-2-({4-[4-(2-hydroxyethyl)piperazin-1-yl]phenyl}amino)pyrimidine-5-carboxamide × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；vapor diffusion, temperature 298K
Resolution 2.30 Å R-free 0.284
3EQP Crystal Structure of Ack1 with compound T95 Deposited 2008-10-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 117–392（276 aa） Fragment：UNP residues 117-392
Not recorded T95 N-(2,6-dimethylphenyl)-4-(2-ethoxyphenoxy)-2-({4-[4-(2-hydroxyethyl)piperazin-1-yl]phenyl}amino)pyrimidine-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；vapor diffusion, temperature 298K
Resolution 2.30 Å R-free 0.284
3EQR Crystal Structure of Ack1 with compound T74 Deposited 2008-10-01 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 117–392（276 aa） Fragment：UNP residues 117-392
Chain B 117–392（276 aa） Fragment：UNP residues 117-392
Not recorded T74 N~3~-(2,6-dimethylphenyl)-1-(3-methoxy-3-methylbutyl)-N~6~-(4-piperazin-1-ylphenyl)-1H-pyrazolo[3,4-d]pyrimidine-3,6-diamine × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；vapor diffusion, temperature 298K
Resolution 2.00 Å R-free 0.256
3EQR Crystal Structure of Ack1 with compound T74 Deposited 2008-10-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 117–392（276 aa） Fragment：UNP residues 117-392
Not recorded T74 N~3~-(2,6-dimethylphenyl)-1-(3-methoxy-3-methylbutyl)-N~6~-(4-piperazin-1-ylphenyl)-1H-pyrazolo[3,4-d]pyrimidine-3,6-diamine × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；vapor diffusion, temperature 298K
Resolution 2.00 Å R-free 0.256
3EQR Crystal Structure of Ack1 with compound T74 Deposited 2008-10-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 117–392（276 aa） Fragment：UNP residues 117-392
Not recorded T74 N~3~-(2,6-dimethylphenyl)-1-(3-methoxy-3-methylbutyl)-N~6~-(4-piperazin-1-ylphenyl)-1H-pyrazolo[3,4-d]pyrimidine-3,6-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；vapor diffusion, temperature 298K
Resolution 2.00 Å R-free 0.256
4EWH Co-crystal structure of ACK1 with inhibitor Deposited 2012-04-27 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 117–391（275 aa）
Chain B 117–391（275 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) T77 6-{4-[2-(dimethylamino)ethoxy]phenyl}-N-(1,3-dithiolan-2-ylmethyl)-5-phenyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；vapor diffusion, temperature 298K
Resolution 2.50 Å R-free 0.313
4HZR Crystal structure of Ack1 kinase domain Deposited 2012-11-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 115–389（275 aa） Fragment：protein kinase domain (UNP residues 115-389)
Not recorded SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；286 K；0.1 M bicine, pH 9.0, 12-15% PEG400, 25 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Resolution 1.31 Å R-free 0.209
4HZR Crystal structure of Ack1 kinase domain Deposited 2012-11-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 115–389（275 aa） Fragment：protein kinase domain (UNP residues 115-389)
Not recorded SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；286 K；0.1 M bicine, pH 9.0, 12-15% PEG400, 25 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Resolution 1.31 Å R-free 0.209
4HZS Crystal structure of Ack1 kinase domain with C-terminal SH3 domain Deposited 2012-11-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 115–453（339 aa） Fragment：protein kinase and SH3 domains (UNP residues 115-453)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；286 K；0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.6, 22-24% PEG3350, 10-20 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Resolution 3.23 Å R-free 0.270
4HZS Crystal structure of Ack1 kinase domain with C-terminal SH3 domain Deposited 2012-11-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 115–453（339 aa） Fragment：protein kinase and SH3 domains (UNP residues 115-453)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；286 K；0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.6, 22-24% PEG3350, 10-20 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Resolution 3.23 Å R-free 0.270
4HZS Crystal structure of Ack1 kinase domain with C-terminal SH3 domain Deposited 2012-11-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 115–453（339 aa） Fragment：protein kinase and SH3 domains (UNP residues 115-453)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；286 K；0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.6, 22-24% PEG3350, 10-20 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Resolution 3.23 Å R-free 0.270
4HZS Crystal structure of Ack1 kinase domain with C-terminal SH3 domain Deposited 2012-11-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 115–453（339 aa） Fragment：protein kinase and SH3 domains (UNP residues 115-453)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；286 K；0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.6, 22-24% PEG3350, 10-20 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Resolution 3.23 Å R-free 0.270
4ID7 ACK1 kinase in complex with the inhibitor cis-3-[8-amino-1-(4-phenoxyphenyl)imidazo[1,5-a]pyrazin-3-yl]cyclobutanol Deposited 2012-12-11 Different construct 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 117–389（273 aa） Fragment：Kinase domain, UNP residues 117-389
Not recorded 1G0 cis-3-[8-amino-1-(4-phenoxyphenyl)imidazo[1,5-a]pyrazin-3-yl]cyclobutanol × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions ligang replacement；ligang replacement
Resolution 3.00 Å R-free 0.259
5ZXB Crystal structure of ACK1 with compound 10d Deposited 2018-05-18 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 117–391（275 aa）
Chain B 117–391（275 aa）
Not recorded 9KO N-{3-[7-{[6-(4-acetylpiperazin-1-yl)pyridin-3-yl]amino}-1-methyl-2-oxo-1,4-dihydropyrimido[4,5-d]pyrimidin-3(2H)-yl]-4-methylphenyl}-3-(trifluoromethyl)benzamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6.3；291 K；0.1M Bis-Tris pH6.3 0.2M AmSO4 28% PEG3350 10mM DTT
Resolution 2.20 Å R-free 0.257
6VQM Crystal Structure Analysis of human ACK1 Deposited 2020-02-05 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 109–395（287 aa）
Chain B 109–395（287 aa）
Not recorded R7P 2-({4-[(3R,5S)-3,5-dimethylpiperazin-1-yl]-2-methoxyphenyl}amino)-9-methyl-5,7-dihydro-6H-pyrimido[5,4-d][1,3]benzodiazepin-6-one × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；PEG4000
Resolution 2.87 Å R-free 0.330
7KP6 Structure of Ack1 kinase in complex with a selective inhibitor Deposited 2020-11-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 110–391（282 aa） Fragment：kinase domain
Not recorded WTP 5-chloro-N~2~-[4-(4-methylpiperazin-1-yl)phenyl]-N~4~-{[(2R)-oxolan-2-yl]methyl}pyrimidine-2,4-diamine × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；50mM Bis-Tris (pH 6.5), 23 % (w/v) polyethylene glycol 3350, 100 mM MgCl2, and 2.5% Glycerol
Resolution 1.79 Å R-free 0.203
7KP6 Structure of Ack1 kinase in complex with a selective inhibitor Deposited 2020-11-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 110–391（282 aa） Fragment：kinase domain
Not recorded WTP 5-chloro-N~2~-[4-(4-methylpiperazin-1-yl)phenyl]-N~4~-{[(2R)-oxolan-2-yl]methyl}pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；50mM Bis-Tris (pH 6.5), 23 % (w/v) polyethylene glycol 3350, 100 mM MgCl2, and 2.5% Glycerol
Resolution 1.79 Å R-free 0.203
8FE9 Crystal structure of Ack1 kinase K161Q mutant in complex with the selective inhibitor (R)-9b Deposited 2022-12-06 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 110–391（282 aa）
Mutation：K161Q WTP 5-chloro-N~2~-[4-(4-methylpiperazin-1-yl)phenyl]-N~4~-{[(2R)-oxolan-2-yl]methyl}pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.05 M Bis-Tris (pH 5.8), 19% PEG3350, 0.3 M MgCl2, 2.5% glycerol
Resolution 3.20 Å R-free 0.228
8FZ3 Sterile Alpha Motif of Human Translocation ETS Leukemia, Non-Polymer Crystal Form Deposited 2023-01-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 958–1038（81 aa）
Mutation：R45S, V77E CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；298 K；1.4 M Sodium phosphate monobasic monohydrate/Potassium phosphate dibasic pH 8.2
Resolution 2.78 Å R-free 0.267
8FZ3 Sterile Alpha Motif of Human Translocation ETS Leukemia, Non-Polymer Crystal Form Deposited 2023-01-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 958–1038（81 aa）
Mutation：R45S, V77E PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；298 K；1.4 M Sodium phosphate monobasic monohydrate/Potassium phosphate dibasic pH 8.2
Resolution 2.78 Å R-free 0.267
8FZ3 Sterile Alpha Motif of Human Translocation ETS Leukemia, Non-Polymer Crystal Form Deposited 2023-01-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain C 958–1038（81 aa）
Mutation：R45S, V77E CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；298 K；1.4 M Sodium phosphate monobasic monohydrate/Potassium phosphate dibasic pH 8.2
Resolution 2.78 Å R-free 0.267
8FZ3 Sterile Alpha Motif of Human Translocation ETS Leukemia, Non-Polymer Crystal Form Deposited 2023-01-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain D 958–1038（81 aa）
Mutation：R45S, V77E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；298 K；1.4 M Sodium phosphate monobasic monohydrate/Potassium phosphate dibasic pH 8.2
Resolution 2.78 Å R-free 0.267
8HMT The complex of ACK1 with the inhibitor 2-142 Deposited 2022-12-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 117–389（273 aa）
Not recorded LWX 6-(2-bromophenyl)-2-[[3-methyl-4-(4-methylpiperazin-1-yl)phenyl]amino]-8-[[(2S)-oxolan-2-yl]methyl]pyrido[2,3-d]pyrimidin-7-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 4000, 0.2M Bis-Tris ph 6.4
Resolution 3.17 Å R-free 0.264
8HMT The complex of ACK1 with the inhibitor 2-142 Deposited 2022-12-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 117–389（273 aa）
Not recorded LWX 6-(2-bromophenyl)-2-[[3-methyl-4-(4-methylpiperazin-1-yl)phenyl]amino]-8-[[(2S)-oxolan-2-yl]methyl]pyrido[2,3-d]pyrimidin-7-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 4000, 0.2M Bis-Tris ph 6.4
Resolution 3.17 Å R-free 0.264
8HMT The complex of ACK1 with the inhibitor 2-142 Deposited 2022-12-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 117–389（273 aa）
Not recorded LWX 6-(2-bromophenyl)-2-[[3-methyl-4-(4-methylpiperazin-1-yl)phenyl]amino]-8-[[(2S)-oxolan-2-yl]methyl]pyrido[2,3-d]pyrimidin-7-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 4000, 0.2M Bis-Tris ph 6.4
Resolution 3.17 Å R-free 0.264
8HMT The complex of ACK1 with the inhibitor 2-142 Deposited 2022-12-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 117–389（273 aa）
Not recorded LWX 6-(2-bromophenyl)-2-[[3-methyl-4-(4-methylpiperazin-1-yl)phenyl]amino]-8-[[(2S)-oxolan-2-yl]methyl]pyrido[2,3-d]pyrimidin-7-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 4000, 0.2M Bis-Tris ph 6.4
Resolution 3.17 Å R-free 0.264
8Q5P Structure of the lysine methyltransferase SETD2 in complex with a peptide derived from human tyrosine kinase ACK1 Deposited 2023-08-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 508–519（12 aa）
Not recorded ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M TRIS pH 8.5, 16%w/v PEG 10000
Resolution 1.81 Å R-free 0.246
8THA 1TEL, non-compressed, double-helical crystal form Deposited 2023-07-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 954–1038（85 aa）
Mutation：V112E,R80S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.5 M Bis-Tris, 0.35 M Mg-Formate, 5 mg/mL protein
Resolution 1.68 Å R-free 0.215

17 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACK1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–289； UniProt 10–296 Author chain B； PDBConstruct 3–289； UniProt 10–296

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 1u4d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1u4d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1u4d
Deposition date deposition_date2004-07-23
Structure title titleStructure of the ACK1 Kinase Domain bound to Debromohymenialdisine
Keywords keywordsTyrosine 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_guinier27.01 Å
Radius of gyration Rg (electron density) rg_electron26.19 Å
Forward intensity I(0) i058697800.00
Molecular weight molecular_weight59824.0 kDa
Excluded volume excluded_volume75044 ų
Envelope volume envelope_volume94302 ų
Hydration-shell volume shell_volume29917 ų
Envelope diameter envelope_diameter86.1 Å
Shell Rg shell_rg33.67 Å
Envelope Rg envelope_rg26.13 Å
Shape Rg shape_rg26.17 Å
Total Rg total_rg27.07 Å
Total atoms total_atoms4205
Residues n_residues520
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 dmax82.8 Å
Rg (real space) rg_real26.95 Å
Rg uncertainty (real space) rg_real_error0.52 Å
I(0) (real space) i0_real5.8700e+07
I(0) uncertainty (real space) i0_real_error8.1730e+05
Rg (reciprocal space) rg_reciprocal26.97 Å
I(0) (reciprocal space) i0_reciprocal58700000.0000
Solution quality estimate total_estimate0.9117
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.5 Å
Skewness Skewness skewness0.240
Kurtosis Kurtosis kurtosis-0.591
Angular range angular_range— – 0.2950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha25970000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.955
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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_idd1u4da_
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_idd1u4db_
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_id1u4dA01
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_id1u4dA02
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_id1u4dB01
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_id1u4dB02
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)