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4o0t

Back pocket flexibility provides group-II PAK selectivity for type 1 kinase inhibitors

Method: X-RAY DIFFRACTION Dmax: 84.4 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine/threonine-protein kinase PAK 1

Homo sapiens

UniProt Q13153

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 249–545 Fragment：unp residues 249-545 2OL 1-({1-(2-aminopyrimidin-4-yl)-2-[(2-methoxyethyl)amino]-1H-benzimidazol-6-yl}ethynyl)cyclohexanol × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；crystals were grown at 19 C from 1.0 uL + 1.0 uL vapor diffusion drops containing 10 mg/mL protein, 1 mM ligand, 0.15 M DL-Malic Acid pH 7.0, 20% - 30% PEG 3350, 4% 1,3-Propanediol and 0.1 M Sodium Malonate, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 2.60 Å R-free 0.265
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 249–545 Fragment：unp residues 249-545 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；crystals were grown at 19 C from 1.0 uL + 1.0 uL vapor diffusion drops containing 10 mg/mL protein, 1 mM ligand, 0.15 M DL-Malic Acid pH 7.0, 20% - 30% PEG 3350, 4% 1,3-Propanediol and 0.1 M Sodium Malonate, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 2.60 Å R-free 0.265
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 249–545 Chain B； UniProt 249–545 Fragment：unp residues 249-545 2OL 1-({1-(2-aminopyrimidin-4-yl)-2-[(2-methoxyethyl)amino]-1H-benzimidazol-6-yl}ethynyl)cyclohexanol × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；crystals were grown at 19 C from 1.0 uL + 1.0 uL vapor diffusion drops containing 10 mg/mL protein, 1 mM ligand, 0.15 M DL-Malic Acid pH 7.0, 20% - 30% PEG 3350, 4% 1,3-Propanediol and 0.1 M Sodium Malonate, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 2.60 Å R-free 0.265

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 4O0T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1F3M CRYSTAL STRUCTURE OF HUMAN SERINE/THREONINE KINASE PAK1 Deposited 2000-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 70–149（80 aa） Fragment：PAK1 AUTOREGULATORY DOMAIN (70-149)
Chain B 70–149（80 aa） Fragment：PAK1 AUTOREGULATORY DOMAIN (70-149)
Chain C 249–545（297 aa） Fragment：KINASE DOMAIN (249-545)
Chain D 249–545（297 aa） Fragment：KINASE DOMAIN (249-545)
Mutation：K299R Mutation：K299R IOD IODIDE ION × 28 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Resolution 2.30 Å R-free 0.258
1YHV Crystal Structure of PAK1 kinase domain with two point mutations (K299R, T423E) Deposited 2005-01-10 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–545（297 aa） Fragment：kinase domain
Mutation：K299R, T423E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG 4000, NaCl, PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 1.80 Å R-free 0.240
1YHW Crystal Structure of PAK1 kinase domain with one point mutations (K299R) Deposited 2005-01-10 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–545（297 aa） Fragment：kinase domain
Mutation：K299R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG 4000, NaCl, PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.243
1ZSG beta PIX-SH3 complexed with an atypical peptide from alpha-PAK Deposited 2005-05-24 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 183–204（22 aa） Fragment：sequence database residues 183-204
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.3；298 K；Ionic strength (raw mmCIF value) 100 mM Na2SO4；Pressure 1
NMR measurement conditions pH 7.3；298 K；Ionic strength (raw mmCIF value) 100 mM Na2SO4；Pressure 1
NMR sample composition 1mM 15N labelled PIX-SH3 complexed with 1.2 mM peptide in 20 mM Na2HPO4/NaH2PO4, pH 7.3, 100mM Na2SO4, 0.05% NaN3, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1mM 15N,13C labelled PIX-SH3 complexed with 1.2 mM peptide in 20 mM Na2HPO4/NaH2PO4, pH 7.3, 100mM Na2SO4, 0.05% NaN3, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
28OQ Protein Kinaze domain PAK1 complexed with NVS inhibitor Deposited 2026-02-11 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 B 249–545（297 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M HEPES pH 7.5, 0.2 M ammonium sulfate , 24 % (w/v) PEG 1357 3350
Resolution 2.28 Å R-free 0.266
28OQ Protein Kinaze domain PAK1 complexed with NVS inhibitor Deposited 2026-02-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–545（297 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 1 A1JZR (3~{S})-3-[(~{Z})-[11-[2,2-bis(fluoranyl)ethyl]-8-chloranyl-3-fluoranyl-5~{H}-benzo[b][1,4]benzodiazepin-6-ylidene]amino]-~{N}-propan-2-yl-pyrrolidine-1-carboxamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M HEPES pH 7.5, 0.2 M ammonium sulfate , 24 % (w/v) PEG 1357 3350
Resolution 2.28 Å R-free 0.266
2HY8 PAK1 complex with ST2001 Deposited 2006-08-04 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 1 249–545（297 aa） Fragment：kinase domain (residues 249-545)
Mutation：K299R, T423E 1ST (5S,6R,7R,9R)-12-HYDROXY-6-METHOXY-5-METHYL-7-(METHYLAMINO)-6,7,8,9-TETRAHYDRO-5H,14H-5,9-EPOXY-4B,9A,15-TRIAZADIBENZO[ B,H]CYCLONONA[1,2,3,4-JKL]CYCLOPENTA[E]-AS-INDACEN-14-ONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1:1 ration of protein and precipitant. Precipitant: 0.13 M PIPES pH 6.5, 1.5 M NaCl, 23% PEG 4000, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.00 Å R-free 0.234
2QME Crystal structure of human RAC3 in complex with CRIB domain of human p21-activated kinase 1 (PAK1) Deposited 2007-07-16 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 I 74–109（36 aa） Fragment：CRIB domain
Not recorded MG MAGNESIUM ION × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl pH 8.5, 2 M (NH4)2S04, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.75 Å R-free 0.192
2QME Crystal structure of human RAC3 in complex with CRIB domain of human p21-activated kinase 1 (PAK1) Deposited 2007-07-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 74–109（36 aa） Fragment：CRIB domain
Not recorded MG MAGNESIUM ION × 2 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl pH 8.5, 2 M (NH4)2S04, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.75 Å R-free 0.192
3DVP Pak1 peptide bound LC8 Deposited 2008-07-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 212–221（10 aa）
Chain D 212–221（10 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, 200 mM NaCl, 27% (w/v) PEG 4000, and 10% 0.1 M (NH4)6CoCl3, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K, temperature 293K
Resolution 2.50 Å R-free 0.263
3FXZ Crystal structure of PAK1 kinase domain with ruthenium complex lambda-FL172 Deposited 2009-01-21 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 249–545（297 aa） Fragment：UNP residues 249-545
Mutation：K299R Non-standard monomer：Yes (specific site not provided by mmCIF) FLL OCTAHEDRAL RU-PYRIDOCARBAZOLE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.1M Tris pH 8.0, 1M NaCl, 25% PEG 4000, 10mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.64 Å R-free 0.218
3FY0 Crystal structure of PAK1 kinase domain with ruthenium complex DW1 Deposited 2009-01-21 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 249–545（297 aa） Fragment：UNP residues 249-545
Mutation：K299R Non-standard monomer：Yes (specific site not provided by mmCIF) DW1 Ruthenium pyridocarbazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M HEPES pH 7.5, 1M NaCl, 25% PEG 10000, 10mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.35 Å R-free 0.260
3Q4Z Structure of unphosphorylated PAK1 kinase domain Deposited 2010-12-26 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 248–545（298 aa） Fragment：kinase domain, UNP residues 248-545
Chain B 248–545（298 aa） Fragment：kinase domain, UNP residues 248-545
Mutation：S259I, K299R, D389N, L516I Mutation：S259I, K299R, D389N, L516I MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1M Hepes pH 7.5, 25% PEG 3350, 0.2M Ammonium Sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 1.89 Å R-free 0.231
3Q52 Structure of phosphorylated PAK1 kinase domain Deposited 2010-12-26 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 248–545（298 aa） Fragment：kinase domain, UNP residues 248-545
Mutation：K299R, L516I Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；25% PEG 3350, 0.2M Na/K Tartrate, 0.1M NDSB256, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 1.80 Å R-free 0.214
3Q53 Structure of phosphorylated PAK1 kinase domain in complex with ATP Deposited 2010-12-26 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 248–545（298 aa） Fragment：kinase domain, UNP residues 248-545
Mutation：K299R, L516I Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；25% PEG 3350, 0.2M Na/K Tartrate, 0.1M NDSB256, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.09 Å R-free 0.223
4DAW Crystal structure of PAK1 kinase domain with the ruthenium phthalimide complex Deposited 2012-01-13 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 249–545（297 aa） Fragment：unp residues 249-545
Mutation：K299R Non-standard monomer：Yes (specific site not provided by mmCIF) 0H2 [1,3-dioxo-6-(pyridin-2-yl-kappaN)-2,3-dihydro-1H-isoindol-5-yl-kappaC~5~][(thioxomethylidene)azanido-kappaN](1,4,7-trithionane-kappa~3~S~1~,S~4~,S~7~)ruthenium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；25 PEG 4000, 1 M NaCl, 10 mM DTT, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.00 Å R-free 0.238
4EQC Crystal structure of PAK1 kinase domain in complex with FRAX597 inhibitor Deposited 2012-04-18 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 249–545（297 aa） Fragment：unp residues 249-545
Mutation：K299R Non-standard monomer：Yes (specific site not provided by mmCIF) XR1 6-[2-chloro-4-(1,3-thiazol-5-yl)phenyl]-8-ethyl-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrido[2,3-d]pyrimidin-7(8H)-one × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M HEPES, 1 M NaCl, 25% PEG 3350, 10 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.01 Å R-free 0.253
4O0R Back pocket flexibility provides group-II PAK selectivity for type 1 kinase inhibitors Deposited 2013-12-14 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–545（297 aa） Fragment：unp residues 249-545
Not recorded 7KC PF-3758309 × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；crystals were grown at 19 C from 1.0 uL + 1.0 uL vapor diffusion drops containing 10 mg/mL protein, 1 mM ligand, 0.15 M DL-Malic Acid, 20% - 30% PEG 3350, 4% 1,3-Propanediol and 0.1 M Sodium Malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.40 Å R-free 0.242
4O0R Back pocket flexibility provides group-II PAK selectivity for type 1 kinase inhibitors Deposited 2013-12-14 Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 249–545（297 aa） Fragment：unp residues 249-545
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；crystals were grown at 19 C from 1.0 uL + 1.0 uL vapor diffusion drops containing 10 mg/mL protein, 1 mM ligand, 0.15 M DL-Malic Acid, 20% - 30% PEG 3350, 4% 1,3-Propanediol and 0.1 M Sodium Malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.40 Å R-free 0.242
4O0R Back pocket flexibility provides group-II PAK selectivity for type 1 kinase inhibitors Deposited 2013-12-14 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 249–545（297 aa） Fragment：unp residues 249-545
Chain B 249–545（297 aa） Fragment：unp residues 249-545
Not recorded 7KC PF-3758309 × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；crystals were grown at 19 C from 1.0 uL + 1.0 uL vapor diffusion drops containing 10 mg/mL protein, 1 mM ligand, 0.15 M DL-Malic Acid, 20% - 30% PEG 3350, 4% 1,3-Propanediol and 0.1 M Sodium Malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.40 Å R-free 0.242
4P90 Crystal structure of the kinase domain of human PAK1 in complex with compound 15 Deposited 2014-04-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–545（297 aa）
Mutation：D389N, T423E, E503D 2K0 [2-chloro-5-(hydroxymethyl)phenyl]{5-[1-(piperidin-4-yl)-1H-pyrazol-4-yl]-1H-pyrrolo[2,3-b]pyridin-3-yl}methanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.2M ammonium sulphate, 16% PEG 3350, 0.1M Hepes (pH 7.6)
Resolution 2.49 Å R-free 0.225
4P90 Crystal structure of the kinase domain of human PAK1 in complex with compound 15 Deposited 2014-04-01 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 249–545（297 aa）
Mutation：D389N, T423E, E503D 2K0 [2-chloro-5-(hydroxymethyl)phenyl]{5-[1-(piperidin-4-yl)-1H-pyrazol-4-yl]-1H-pyrrolo[2,3-b]pyridin-3-yl}methanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.2M ammonium sulphate, 16% PEG 3350, 0.1M Hepes (pH 7.6)
Resolution 2.49 Å R-free 0.225
4ZJI PAK1 in complex with 2-chloro-5-ethyl-8-fluoro-11-(4-methylpiperazin-1-yl)-dibenzodiazepine Deposited 2015-04-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–545（297 aa）
Not recorded 4OQ 2-chloro-5-ethyl-8-fluoro-11-(4-methylpiperazin-1-yl)-dibenzodiazepine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；Equal volumes (1.0 uL) of reservoir solution and protein solution were mixed. Reservoir solution: 17.2% (w/v) PEG3350, 0.2 M magnesium formate (dihydrate)
Resolution 1.99 Å R-free 0.220
4ZJI PAK1 in complex with 2-chloro-5-ethyl-8-fluoro-11-(4-methylpiperazin-1-yl)-dibenzodiazepine Deposited 2015-04-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 249–545（297 aa）
Not recorded 4OQ 2-chloro-5-ethyl-8-fluoro-11-(4-methylpiperazin-1-yl)-dibenzodiazepine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；Equal volumes (1.0 uL) of reservoir solution and protein solution were mixed. Reservoir solution: 17.2% (w/v) PEG3350, 0.2 M magnesium formate (dihydrate)
Resolution 1.99 Å R-free 0.220
4ZJI PAK1 in complex with 2-chloro-5-ethyl-8-fluoro-11-(4-methylpiperazin-1-yl)-dibenzodiazepine Deposited 2015-04-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 249–545（297 aa）
Not recorded 4OQ 2-chloro-5-ethyl-8-fluoro-11-(4-methylpiperazin-1-yl)-dibenzodiazepine × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；Equal volumes (1.0 uL) of reservoir solution and protein solution were mixed. Reservoir solution: 17.2% (w/v) PEG3350, 0.2 M magnesium formate (dihydrate)
Resolution 1.99 Å R-free 0.220
4ZJI PAK1 in complex with 2-chloro-5-ethyl-8-fluoro-11-(4-methylpiperazin-1-yl)-dibenzodiazepine Deposited 2015-04-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 249–545（297 aa）
Not recorded 4OQ 2-chloro-5-ethyl-8-fluoro-11-(4-methylpiperazin-1-yl)-dibenzodiazepine × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；Equal volumes (1.0 uL) of reservoir solution and protein solution were mixed. Reservoir solution: 17.2% (w/v) PEG3350, 0.2 M magnesium formate (dihydrate)
Resolution 1.99 Å R-free 0.220
4ZJJ PAK1 in complex with (S)-N-(tert-butyl)-3-((2-chloro-5-ethyl-8-fluoro-dibenzodiazepin-11-yl)amino)pyrrolidine-1-carboxamide Deposited 2015-04-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–545（297 aa）
Not recorded 4OR (S)-N-(tert-butyl)-3-((2-chloro-5-ethyl-8-fluoro-dibenzodiazepin-11-yl)amino)pyrrolidine-1-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；Equal volumes (0.8 uL) of reservoir solution and protein solution were mixed. Reservoir solution: 16.8% (w/v) PEG3350, 0.2 M magnesium formate (dihydrate)
Resolution 2.20 Å R-free 0.238
4ZJJ PAK1 in complex with (S)-N-(tert-butyl)-3-((2-chloro-5-ethyl-8-fluoro-dibenzodiazepin-11-yl)amino)pyrrolidine-1-carboxamide Deposited 2015-04-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 249–545（297 aa）
Not recorded 4OR (S)-N-(tert-butyl)-3-((2-chloro-5-ethyl-8-fluoro-dibenzodiazepin-11-yl)amino)pyrrolidine-1-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；Equal volumes (0.8 uL) of reservoir solution and protein solution were mixed. Reservoir solution: 16.8% (w/v) PEG3350, 0.2 M magnesium formate (dihydrate)
Resolution 2.20 Å R-free 0.238
4ZJJ PAK1 in complex with (S)-N-(tert-butyl)-3-((2-chloro-5-ethyl-8-fluoro-dibenzodiazepin-11-yl)amino)pyrrolidine-1-carboxamide Deposited 2015-04-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 249–545（297 aa）
Not recorded 4OR (S)-N-(tert-butyl)-3-((2-chloro-5-ethyl-8-fluoro-dibenzodiazepin-11-yl)amino)pyrrolidine-1-carboxamide × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；Equal volumes (0.8 uL) of reservoir solution and protein solution were mixed. Reservoir solution: 16.8% (w/v) PEG3350, 0.2 M magnesium formate (dihydrate)
Resolution 2.20 Å R-free 0.238
4ZJJ PAK1 in complex with (S)-N-(tert-butyl)-3-((2-chloro-5-ethyl-8-fluoro-dibenzodiazepin-11-yl)amino)pyrrolidine-1-carboxamide Deposited 2015-04-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 249–545（297 aa）
Not recorded 4OR (S)-N-(tert-butyl)-3-((2-chloro-5-ethyl-8-fluoro-dibenzodiazepin-11-yl)amino)pyrrolidine-1-carboxamide × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；Equal volumes (0.8 uL) of reservoir solution and protein solution were mixed. Reservoir solution: 16.8% (w/v) PEG3350, 0.2 M magnesium formate (dihydrate)
Resolution 2.20 Å R-free 0.238
4ZLO Serine/threonine-protein kinase PAK1 complexed with a dibenzodiazepine: identification of an allosteric site on PAK1 Deposited 2015-05-01 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 249–545（297 aa）
Chain B 249–545（297 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 4PV 2,8-difluoro-11-(4-methylpiperazin-1-yl)-5H-dibenzo[b,e][1,4]diazepine × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；22-27% PEG3350, 500-700MM NACL, 100MM BIS-TRIS, PH 6.5
Resolution 2.50 Å R-free 0.222
4ZLO Serine/threonine-protein kinase PAK1 complexed with a dibenzodiazepine: identification of an allosteric site on PAK1 Deposited 2015-05-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 249–545（297 aa）
Chain B 249–545（297 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 4PV 2,8-difluoro-11-(4-methylpiperazin-1-yl)-5H-dibenzo[b,e][1,4]diazepine × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；22-27% PEG3350, 500-700MM NACL, 100MM BIS-TRIS, PH 6.5
Resolution 2.50 Å R-free 0.222
4ZY4 Crystal structure of P21 activated kinase 1 in complex with an inhibitor compound 4 Deposited 2015-05-21 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 249–545（297 aa） Fragment：Protein kinase domain residue 249-545
Mutation：D389N 4T3 2-(4-aminopiperidin-1-yl)-N-(5-cyclopropyl-1H-pyrazol-3-yl)thieno[3,2-d]pyrimidin-4-amine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；25% PEG 3500, 0.2M Ammonium Sulfate and 0.1M Tris pH 8
Resolution 2.60 Å R-free 0.248
4ZY4 Crystal structure of P21 activated kinase 1 in complex with an inhibitor compound 4 Deposited 2015-05-21 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 249–545（297 aa） Fragment：Protein kinase domain residue 249-545
Mutation：D389N 4T3 2-(4-aminopiperidin-1-yl)-N-(5-cyclopropyl-1H-pyrazol-3-yl)thieno[3,2-d]pyrimidin-4-amine × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；25% PEG 3500, 0.2M Ammonium Sulfate and 0.1M Tris pH 8
Resolution 2.60 Å R-free 0.248
4ZY5 Crystal Structure of p21-activated kinase 1 in complex with an inhibitor compound 17 Deposited 2015-05-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–545（297 aa） Fragment：Protein kinase domain residue 249-545
Not recorded 4T5 N~2~-[(trans-4-aminocyclohexyl)methyl]-N~4~-(3-cyclopropyl-1H-pyrazol-5-yl)pyrimidine-2,4-diamine × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；25% PEG 3500, 0.2M Ammonium Sulfate and 0.1M Tris pH 8
Resolution 2.35 Å R-free 0.230
4ZY5 Crystal Structure of p21-activated kinase 1 in complex with an inhibitor compound 17 Deposited 2015-05-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 249–545（297 aa） Fragment：Protein kinase domain residue 249-545
Not recorded 4T5 N~2~-[(trans-4-aminocyclohexyl)methyl]-N~4~-(3-cyclopropyl-1H-pyrazol-5-yl)pyrimidine-2,4-diamine × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；25% PEG 3500, 0.2M Ammonium Sulfate and 0.1M Tris pH 8
Resolution 2.35 Å R-free 0.230
4ZY6 Crystal structure of P21-activated kinase 1 in complex with an inhibitor compound 29 Deposited 2015-05-21 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 249–545（297 aa） Fragment：Protein kinase domain residue 249-545
Mutation：D389N 4T6 N~2~-[(7-chloro-1H-benzimidazol-6-yl)methyl]-N~4~-(5-cyclopropyl-1H-pyrazol-3-yl)pyrimidine-2,4-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；25% PEG 3500, 0.2M Ammonium Sulfate and 0.1M Tris pH 8
Resolution 2.15 Å R-free 0.239
4ZY6 Crystal structure of P21-activated kinase 1 in complex with an inhibitor compound 29 Deposited 2015-05-21 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 249–545（297 aa） Fragment：Protein kinase domain residue 249-545
Mutation：D389N 4T6 N~2~-[(7-chloro-1H-benzimidazol-6-yl)methyl]-N~4~-(5-cyclopropyl-1H-pyrazol-3-yl)pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；25% PEG 3500, 0.2M Ammonium Sulfate and 0.1M Tris pH 8
Resolution 2.15 Å R-free 0.239
5DEW Crystal structure of PAK1 in complex with an inhibitor compound 5 Deposited 2015-08-26 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–545（297 aa） Fragment：Protein kinase domain residue 249-545
Mutation：D389N, T423E 59N 8-[(trans-4-aminocyclohexyl)methyl]-6-[2-chloro-4-(6-methylpyrazin-2-yl)phenyl]-2-(ethylamino)pyrido[2,3-d]pyrimidin-7(8H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；crystals were grown at 19 C from 1.0 uL + 1.0 uL vapor diffusion drops containing 10 mg/mL protein, 1 mM ligand, 0.15 M DL-Malic Acid pH 7.0, 20% - 30% PEG 3350, 4% 1,3-Propanediol and 0.1 M Sodium Malonate, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 1.90 Å R-free 0.215
5DEW Crystal structure of PAK1 in complex with an inhibitor compound 5 Deposited 2015-08-26 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 249–545（297 aa） Fragment：Protein kinase domain residue 249-545
Mutation：D389N, T423E 59N 8-[(trans-4-aminocyclohexyl)methyl]-6-[2-chloro-4-(6-methylpyrazin-2-yl)phenyl]-2-(ethylamino)pyrido[2,3-d]pyrimidin-7(8H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；crystals were grown at 19 C from 1.0 uL + 1.0 uL vapor diffusion drops containing 10 mg/mL protein, 1 mM ligand, 0.15 M DL-Malic Acid pH 7.0, 20% - 30% PEG 3350, 4% 1,3-Propanediol and 0.1 M Sodium Malonate, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 1.90 Å R-free 0.215
5DEY Crystal structure of PAK1 in complex with an inhibitor compound G-5555 Deposited 2015-08-26 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 249–545（297 aa） Fragment：Protein kinase domain residue 249-545
Mutation：D389N, T423E 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；292 K；crystals were grown at 19 C from 1.0 uL + 1.0 uL vapor diffusion drops containing 10 mg/mL protein, 1 mM ligand, 0.15 M DL-Malic Acid pH 7.0, 20% - 30% PEG 3350, 4% 1,3-Propanediol and 0.1 M Sodium Malonate, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.10 Å R-free 0.228
5DEY Crystal structure of PAK1 in complex with an inhibitor compound G-5555 Deposited 2015-08-26 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 249–545（297 aa） Fragment：Protein kinase domain residue 249-545
Mutation：D389N, T423E 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；292 K；crystals were grown at 19 C from 1.0 uL + 1.0 uL vapor diffusion drops containing 10 mg/mL protein, 1 mM ligand, 0.15 M DL-Malic Acid pH 7.0, 20% - 30% PEG 3350, 4% 1,3-Propanediol and 0.1 M Sodium Malonate, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.10 Å R-free 0.228
5DFP Crystal structure of PAK1 in complex with an inhibitor compound FRAX1036 Deposited 2015-08-27 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 249–545（297 aa） Fragment：Protein kinase domain residue 249-545
Mutation：K299R Non-standard monomer：Yes (specific site not provided by mmCIF) 59U 6-[2-chloro-4-(6-methylpyrazin-2-yl)phenyl]-8-ethyl-2-{[2-(1-methylpiperidin-4-yl)ethyl]amino}pyrido[2,3-d]pyrimidin-7(8H)-one × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1 uL of PAK1 (9 mg/ml) with 1 uL of crystallization solution (0.1 M HEPES pH 7.0, 1 M NaCl, 25% PEG 3350, 10 mM DTT) at 4C
Resolution 2.20 Å R-free 0.246
5IME Crystal structure of P21-activated kinase 1 (PAK1) in complex with compound 9 Deposited 2016-03-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–545（297 aa） Fragment：residues 249-545
Not recorded 6BZ 8-(3-aminopropyl)-6-[2-chloro-4-(3-methyl-2-oxopyrazin-1(2H)-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；crystals were grown at 19 C from 1.0 uL + 1.0 uL vapor diffusion drops containing 10 mg/mL protein, 1 mM ligand, 0.15 M DL-Malic Acid, 20% - 30% PEG 3350, 4% 1,3-Propanediol and 0.1 M Sodium Malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.22 Å R-free 0.263
5IME Crystal structure of P21-activated kinase 1 (PAK1) in complex with compound 9 Deposited 2016-03-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 249–545（297 aa） Fragment：residues 249-545
Not recorded 6BZ 8-(3-aminopropyl)-6-[2-chloro-4-(3-methyl-2-oxopyrazin-1(2H)-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；crystals were grown at 19 C from 1.0 uL + 1.0 uL vapor diffusion drops containing 10 mg/mL protein, 1 mM ligand, 0.15 M DL-Malic Acid, 20% - 30% PEG 3350, 4% 1,3-Propanediol and 0.1 M Sodium Malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.22 Å R-free 0.263
5KBQ Pak1 in complex with bis-anilino pyrimidine inhibitor Deposited 2016-06-03 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 254–542（289 aa）
Mutation：D389N, T423E, E503D IPV [4-methyl-3-[methyl-[2-[(3-methylsulfonyl-5-morpholin-4-yl-phenyl)amino]pyrimidin-4-yl]amino]phenyl]methanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.2M ammonium sulphate, 16% PEG 3350, 0.1M Hepes (pH 7.6)
Resolution 2.58 Å R-free 0.230
5KBQ Pak1 in complex with bis-anilino pyrimidine inhibitor Deposited 2016-06-03 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 254–542（289 aa）
Mutation：D389N, T423E, E503D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.2M ammonium sulphate, 16% PEG 3350, 0.1M Hepes (pH 7.6)
Resolution 2.58 Å R-free 0.230
5KBR Pak1 in complex with 7-azaindole inhibitor Deposited 2016-06-03 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 254–542（289 aa）
Mutation：D389N, T423E, E503D IPW (4-chlorophenyl)-[5-(1-piperidin-4-ylpyrazol-4-yl)-1~{H}-pyrrolo[2,3-b]pyridin-3-yl]methanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.2M ammonium sulphate, 16% PEG 3350, 0.1M Hepes (pH 7.6)
Resolution 2.36 Å R-free 0.255
5KBR Pak1 in complex with 7-azaindole inhibitor Deposited 2016-06-03 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 254–542（289 aa）
Mutation：D389N, T423E, E503D IPW (4-chlorophenyl)-[5-(1-piperidin-4-ylpyrazol-4-yl)-1~{H}-pyrrolo[2,3-b]pyridin-3-yl]methanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.2M ammonium sulphate, 16% PEG 3350, 0.1M Hepes (pH 7.6)
Resolution 2.36 Å R-free 0.255
6B16 P21-activated kinase 1 in complex with a 4-azaindole inhibitor Deposited 2017-09-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–545（297 aa） Fragment：UNP residues 249-545
Not recorded C7Y N~4~-(5-cyclopropyl-1H-pyrazol-3-yl)-N~2~-[(1S)-1-(1H-pyrrolo[3,2-b]pyridin-5-yl)ethyl]pyrimidine-2,4-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；25% PEG 3500, 0.2M Ammonium Sulfate and 0.1M Tris pH 8
Resolution 2.29 Å R-free 0.250
6B16 P21-activated kinase 1 in complex with a 4-azaindole inhibitor Deposited 2017-09-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 249–545（297 aa） Fragment：UNP residues 249-545
Not recorded C7Y N~4~-(5-cyclopropyl-1H-pyrazol-3-yl)-N~2~-[(1S)-1-(1H-pyrrolo[3,2-b]pyridin-5-yl)ethyl]pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；25% PEG 3500, 0.2M Ammonium Sulfate and 0.1M Tris pH 8
Resolution 2.29 Å R-free 0.250
7VTO The crystal structure of PAK1 with the inhibitor GW8510 Deposited 2021-10-30 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 249–545（297 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 107 4-[(7-OXO-7H-THIAZOLO[5,4-E]INDOL-8-YLMETHYL)-AMINO]-N-PYRIDIN-2-YL-BENZENESULFONAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1 M Tris pH 8.5, 0.2 MgCl2, 24% PEG 3350, 5 mM TCEP
Resolution 2.59 Å R-free 0.252
7VTO The crystal structure of PAK1 with the inhibitor GW8510 Deposited 2021-10-30 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 249–545（297 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 107 4-[(7-OXO-7H-THIAZOLO[5,4-E]INDOL-8-YLMETHYL)-AMINO]-N-PYRIDIN-2-YL-BENZENESULFONAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1 M Tris pH 8.5, 0.2 MgCl2, 24% PEG 3350, 5 mM TCEP
Resolution 2.59 Å R-free 0.252
8X5Z The Crystal Structure of PAK1 kinase domain from Biortus. Deposited 2023-11-20 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–545（297 aa）
Mutation：K299R,E503D Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M SPG pH6.0, 25% PEG 1500
Resolution 1.80 Å R-free 0.216
9D4V Structure of PAK1 in complex with compound 7 Deposited 2024-08-13 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 249–476（228 aa）
Chain A 477–545（69 aa）
Mutation：D389N,T423E Mutation：D389N,T423E A1A2P N~2~-{[(1s,4s)-4-aminocyclohexyl]methyl}-N~4~-(5-cyclopropyl-1,3-thiazol-2-yl)pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.2 M Na-malonate, pH 7.0, 0.15 M DL-malic acid, 4% propane-diol, and 16% PEG 3350
Resolution 1.84 Å R-free 0.269
9D4V Structure of PAK1 in complex with compound 7 Deposited 2024-08-13 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 249–476（228 aa）
Chain B 477–545（69 aa）
Mutation：D389N,T423E Mutation：D389N,T423E A1A2P N~2~-{[(1s,4s)-4-aminocyclohexyl]methyl}-N~4~-(5-cyclopropyl-1,3-thiazol-2-yl)pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.2 M Na-malonate, pH 7.0, 0.15 M DL-malic acid, 4% propane-diol, and 16% PEG 3350
Resolution 1.84 Å R-free 0.269
9D4W Structure of PAK1 in complex with compound 12 Deposited 2024-08-13 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 249–545（297 aa）
Mutation：D389N, T423E A1A2Q N~2~-{[(1s,4s)-4-aminocyclohexyl]methyl}-N~4~-[5-(trifluoromethyl)-1,3-thiazol-2-yl]pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；0.1 M Na-malonate buffer, pH 6.6 , 0.15 M DL-malic acid, 4% propanediol, and 20% PEG 3350
Resolution 2.22 Å R-free 0.232
9D4W Structure of PAK1 in complex with compound 12 Deposited 2024-08-13 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 249–545（297 aa）
Mutation：D389N, T423E A1A2Q N~2~-{[(1s,4s)-4-aminocyclohexyl]methyl}-N~4~-[5-(trifluoromethyl)-1,3-thiazol-2-yl]pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；0.1 M Na-malonate buffer, pH 6.6 , 0.15 M DL-malic acid, 4% propanediol, and 20% PEG 3350
Resolution 2.22 Å R-free 0.232
9D4X Structure of PAK1 in complex with compound 16 Deposited 2024-08-13 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 250–545（296 aa）
Mutation：D389N, T423E A1A2S N~2~-{[(1R,3R,4S)-4-amino-3-(3-chlorophenyl)cyclohexyl]methyl}-N~4~-(5-cyclopropyl-1,3-thiazol-2-yl)pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Na-malonate buffer, pH 6.8 , 0.15 M DL-malic acid, 4% propanediol, and 20% PEG 3350
Resolution 1.85 Å R-free 0.227
9D4X Structure of PAK1 in complex with compound 16 Deposited 2024-08-13 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 250–545（296 aa）
Mutation：D389N, T423E A1A2S N~2~-{[(1R,3R,4S)-4-amino-3-(3-chlorophenyl)cyclohexyl]methyl}-N~4~-(5-cyclopropyl-1,3-thiazol-2-yl)pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Na-malonate buffer, pH 6.8 , 0.15 M DL-malic acid, 4% propanediol, and 20% PEG 3350
Resolution 1.85 Å R-free 0.227
9D4Y Structure of PAK1 in complex with compound 31 Deposited 2024-08-13 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 249–545（297 aa）
Mutation：D389N, T423E A1A2S N~2~-{[(1R,3R,4S)-4-amino-3-(3-chlorophenyl)cyclohexyl]methyl}-N~4~-(5-cyclopropyl-1,3-thiazol-2-yl)pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；100 mM malonate pH 6.6, 150 mM malic acid, 22% PEG 3350, 4% 1,2-propanediol
Resolution 1.85 Å R-free 0.227
9D4Y Structure of PAK1 in complex with compound 31 Deposited 2024-08-13 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 249–545（297 aa）
Mutation：D389N, T423E A1A2S N~2~-{[(1R,3R,4S)-4-amino-3-(3-chlorophenyl)cyclohexyl]methyl}-N~4~-(5-cyclopropyl-1,3-thiazol-2-yl)pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；100 mM malonate pH 6.6, 150 mM malic acid, 22% PEG 3350, 4% 1,2-propanediol
Resolution 1.85 Å R-free 0.227
9D50 Structure of PAK1 in complex with compound 24 Deposited 2024-08-13 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 250–545（296 aa）
Mutation：D389N, T423E A1A2T 3-cyano-N-[3-({6-[(5-cyclopropyl-1,3-thiazol-2-yl)amino]pyrazin-2-yl}amino)bicyclo[1.1.1]pentan-1-yl]azetidine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM malonate pH 6.6, 150 mM malic acid, 19% PEG 3350, 4% 1,2-propanediol
Resolution 1.90 Å R-free 0.230
9D50 Structure of PAK1 in complex with compound 24 Deposited 2024-08-13 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 250–545（296 aa）
Mutation：D389N, T423E A1A2T 3-cyano-N-[3-({6-[(5-cyclopropyl-1,3-thiazol-2-yl)amino]pyrazin-2-yl}amino)bicyclo[1.1.1]pentan-1-yl]azetidine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM malonate pH 6.6, 150 mM malic acid, 19% PEG 3350, 4% 1,2-propanediol
Resolution 1.90 Å R-free 0.230
9N48 Crystal structure of PAK1 bound to compound C1 Deposited 2025-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 249–545（297 aa）
Chain B 249–545（297 aa）
Not recorded A1BV1 (6M)-8-[2-(2-aminoethoxy)ethyl]-6-[2-chloro-3-fluoro-4-(2-oxopyrrolidin-1-yl)phenyl]-2-(ethylamino)pyrido[2,3-d]pyrimidin-7(8H)-one × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.2 M Lithium Sulfate, 0.1 M Tris pH8.5, 30% PEG4000
Resolution 1.85 Å R-free 0.216
9N4U Crystal structure of PAK1 bound to compound R1 Deposited 2025-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 249–545（297 aa）
Chain B 249–545（297 aa）
Not recorded A1BV8 (3M)-3-[(4P)-2-chloro-4-(6-methylpyridin-2-yl)phenyl]-1-{2-[2-(dimethylamino)ethoxy]ethyl}-1,6-naphthyridin-2(1H)-one × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Lithium Sulfate, 0.1M Tris pH 8.5, 30% PEG4000
Resolution 1.77 Å R-free 0.203
9NBX Crystal structure of PAK1 bound to C2 Deposited 2025-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 249–545（297 aa）
Chain B 249–545（297 aa）
Not recorded A1BW5 (6M)-8-(3-aminopropyl)-6-(4-butoxy-2-methylphenyl)-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one × 2 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Lithium Sulfate, 0.1M Tris pH8.5, 30% PEG 4000
Resolution 2.15 Å R-free 0.265

40 other PDB entries and 67 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PAK1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–297； UniProt 249–545 Author chain B； PDBConstruct 1–297； UniProt 249–545

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 4o0t

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4o0t
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4o0t
Deposition date deposition_date2013-12-14
Structure title titleBack pocket flexibility provides group-II PAK selectivity for type 1 kinase inhibitors
Keywords keywordsPAK1, 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_guinier27.64 Å
Radius of gyration Rg (electron density) rg_electron26.68 Å
Forward intensity I(0) i064752400.00
Molecular weight molecular_weight63708.0 kDa
Excluded volume excluded_volume80366 ų
Envelope volume envelope_volume102520 ų
Hydration-shell volume shell_volume32229 ų
Envelope diameter envelope_diameter87.7 Å
Shell Rg shell_rg33.90 Å
Envelope Rg envelope_rg26.05 Å
Shape Rg shape_rg26.67 Å
Total Rg total_rg27.54 Å
Total atoms total_atoms4466
Residues n_residues572
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 dmax84.4 Å
Rg (real space) rg_real27.52 Å
Rg uncertainty (real space) rg_real_error0.56 Å
I(0) (real space) i0_real6.4750e+07
I(0) uncertainty (real space) i0_real_error8.4400e+05
Rg (reciprocal space) rg_reciprocal27.56 Å
I(0) (reciprocal space) i0_reciprocal64750000.0000
Solution quality estimate total_estimate0.9125
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.1 Å
Skewness Skewness skewness0.170
Kurtosis Kurtosis kurtosis-0.604
Angular range angular_range— – 0.2850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha24790000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.969; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.952
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4o0ta_
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_idd4o0tb_
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_id4o0tA01
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_id4o0tA02
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_id4o0tB01
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_id4o0tB02
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)