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- PDB-9d50: Structure of PAK1 in complex with compound 24 -

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Basic information

Entry
Database: PDB / ID: 9d50
TitleStructure of PAK1 in complex with compound 24
ComponentsSerine/threonine-protein kinase PAK 1
KeywordsTRANSFERASE / Serine/threonine-protein kinase / inhibitor
Function / homology
Function and homology information


negative regulation of cell proliferation involved in contact inhibition / protein localization to cytoplasmic stress granule / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / gamma-tubulin binding / RHO GTPases Activate ROCKs / positive regulation of vascular associated smooth muscle cell migration / Activation of RAC1 / Ephrin signaling ...negative regulation of cell proliferation involved in contact inhibition / protein localization to cytoplasmic stress granule / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / gamma-tubulin binding / RHO GTPases Activate ROCKs / positive regulation of vascular associated smooth muscle cell migration / Activation of RAC1 / Ephrin signaling / CD28 dependent Vav1 pathway / positive regulation of fibroblast migration / regulation of axonogenesis / RHOV GTPase cycle / positive regulation of intracellular estrogen receptor signaling pathway / branching morphogenesis of an epithelial tube / RHOJ GTPase cycle / establishment of cell polarity / stimulatory C-type lectin receptor signaling pathway / RHOQ GTPase cycle / Fc-gamma receptor signaling pathway involved in phagocytosis / exocytosis / RHO GTPases activate PAKs / RHOU GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / Generation of second messenger molecules / intercalated disc / RHOH GTPase cycle / Sema3A PAK dependent Axon repulsion / positive regulation of protein targeting to membrane / Smooth Muscle Contraction / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of insulin receptor signaling pathway / ephrin receptor signaling pathway / positive regulation of axon extension / collagen binding / positive regulation of vascular associated smooth muscle cell proliferation / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / neuron projection morphogenesis / ruffle / positive regulation of microtubule polymerization / RAC1 GTPase cycle / EPHB-mediated forward signaling / CD209 (DC-SIGN) signaling / cerebellum development / cellular response to starvation / Signal transduction by L1 / VEGFR2 mediated vascular permeability / regulation of actin cytoskeleton organization / actin filament / FCERI mediated MAPK activation / wound healing / MAPK6/MAPK4 signaling / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / Z disc / cellular response to insulin stimulus / G beta:gamma signalling through CDC42 / cell-cell junction / cell migration / lamellipodium / chromosome / actin cytoskeleton organization / nuclear membrane / response to hypoxia / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / chromatin remodeling / axon / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / dendrite / centrosome / protein kinase binding / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Serine/threonine-protein kinase PAK 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 Å
AuthorsFontano, E. / Suto, R.K. / Olland, A.M.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2025
Title: Identification of a p21-activated kinase 1 (PAK1) inhibitor with 10-fold selectivity against PAK2.
Authors: Johns, D.M. / Olejniczak, J. / Babbar, A. / Boone, C.D. / Cakici, O. / Cheng, M. / Cheng, Q.Q. / Dementiev, A. / Eick, M. / Ferdyan, N. / Fontano, E. / Forman, A. / Kozlowski, R. / Lee, S.W. ...Authors: Johns, D.M. / Olejniczak, J. / Babbar, A. / Boone, C.D. / Cakici, O. / Cheng, M. / Cheng, Q.Q. / Dementiev, A. / Eick, M. / Ferdyan, N. / Fontano, E. / Forman, A. / Kozlowski, R. / Lee, S.W. / Mehta, S. / Mowery, K. / Murray, B. / Nguyen, V. / Olland, A. / Phan, K.B. / Rivera, L. / Sabat, M. / Sprengeler, P. / Srinivasan, K. / Sun, Z. / Suto, R.K. / Wilkinson, T. / Wang, C. / Yu, N. / Xu, M. / Goel, V. / Hirst, G. / Reich, S.
History
DepositionAug 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 16, 2025Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PAK 1
B: Serine/threonine-protein kinase PAK 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2434
Polymers66,3982
Non-polymers8452
Water3,225179
1
A: Serine/threonine-protein kinase PAK 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6222
Polymers33,1991
Non-polymers4231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase PAK 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6222
Polymers33,1991
Non-polymers4231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.267, 80.951, 65.634
Angle α, β, γ (deg.)90, 108.797, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase PAK 1 / Alpha-PAK / p21-activated kinase 1 / PAK-1 / p65-PAK


Mass: 33199.191 Da / Num. of mol.: 2 / Mutation: D389N, T423E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13153, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-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


Mass: 422.507 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N8OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM malonate pH 6.6, 150 mM malic acid, 19% PEG 3350, 4% 1,2-propanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.898→54.213 Å / Num. obs: 44800 / % possible obs: 99.8 % / Redundancy: 5.51 % / CC1/2: 0.997 / Net I/σ(I): 9.8
Reflection shellResolution: 1.898→1.93 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2233 / CC1/2: 0.564

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.898→54.213 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.68 / SU ML: 0.122 / Cross valid method: FREE R-VALUE / ESU R: 0.155 / ESU R Free: 0.146
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2299 2331 5.203 %
Rwork0.1839 42468 -
all0.186 --
obs-44799 99.791 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 47.126 Å2
Baniso -1Baniso -2Baniso -3
1-0.037 Å2-0 Å20.106 Å2
2--0.051 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.898→54.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4339 0 60 179 4578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124498
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164293
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.846115
X-RAY DIFFRACTIONr_angle_other_deg0.5561.7529922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5895572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.679527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41410781
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.27110177
X-RAY DIFFRACTIONr_chiral_restr0.0870.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025214
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02946
X-RAY DIFFRACTIONr_nbd_refined0.2090.2937
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.23899
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22239
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22337
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2176
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.180.219
X-RAY DIFFRACTIONr_nbd_other0.2280.297
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.28
X-RAY DIFFRACTIONr_mcbond_it3.1173.832282
X-RAY DIFFRACTIONr_mcbond_other3.1133.832282
X-RAY DIFFRACTIONr_mcangle_it4.3336.8592847
X-RAY DIFFRACTIONr_mcangle_other4.3326.8592848
X-RAY DIFFRACTIONr_scbond_it4.2314.2262216
X-RAY DIFFRACTIONr_scbond_other4.234.2272217
X-RAY DIFFRACTIONr_scangle_it6.2977.5793245
X-RAY DIFFRACTIONr_scangle_other6.2967.583246
X-RAY DIFFRACTIONr_lrange_it7.76839.3925010
X-RAY DIFFRACTIONr_lrange_other7.77439.0044984
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.898-1.9470.3331520.29831270.332840.9220.93599.84770.269
1.947-20.2941680.26930550.2732250.9340.94999.9380.241
2-2.0580.2891870.24229420.24531300.9480.96199.9680.214
2.058-2.1210.2851590.23229060.23430680.9420.96699.90220.208
2.121-2.1910.2211310.20527940.20629290.9680.97399.86340.179
2.191-2.2680.2381500.19827070.228600.9650.97699.89510.181
2.268-2.3530.2221420.18225730.18427220.9680.98199.74280.167
2.353-2.4490.281330.17325320.17826670.9590.98299.9250.16
2.449-2.5580.2691550.17723860.18225430.9620.98299.92130.166
2.558-2.6820.2711230.19423200.19824450.9580.97999.91820.189
2.682-2.8270.2711110.1921820.19322980.960.9899.78240.19
2.827-2.9980.2571140.19421070.19722290.9620.97899.64110.202
2.998-3.2040.2691110.18319320.18720510.9560.97999.60990.194
3.204-3.460.211880.17818350.1819290.9720.98199.6890.196
3.46-3.7880.211950.16316820.16617810.9750.98499.77540.189
3.788-4.2330.175780.15915090.1615910.980.98599.74860.191
4.233-4.8830.195690.15513450.15714200.9760.98699.57750.192
4.883-5.9680.221770.17911420.18212280.9750.98399.26710.236
5.968-8.390.221590.1798750.1829420.970.98199.15070.235
8.39-54.2130.195290.25160.25490.9810.9899.27140.257
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.85510.1237-0.16940.78620.21951.24570.04420.0068-0.022-0.0209-0.0656-0.0340.04530.00310.02140.040.0131-0.02630.0089-0.00430.025521.2482-5.634416.3413
21.1384-0.02250.0080.4016-0.03270.5239-0.0386-0.09290.01390.04380.01630.01640.041-0.01950.02230.0288-0.0097-0.00960.0408-0.00970.023110.2704-0.3902-16.3736
Refinement TLS groupSelection: ALL

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