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- PDB-9d4x: Structure of PAK1 in complex with compound 16 -

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Basic information

Entry
Database: PDB / ID: 9d4x
TitleStructure of PAK1 in complex with compound 16
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 / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / RHO GTPases Activate ROCKs / gamma-tubulin binding / Activation of RAC1 / Ephrin signaling / CD28 dependent Vav1 pathway / regulation of axonogenesis ...negative regulation of cell proliferation involved in contact inhibition / protein localization to cytoplasmic stress granule / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / RHO GTPases Activate ROCKs / gamma-tubulin binding / Activation of RAC1 / Ephrin signaling / CD28 dependent Vav1 pathway / regulation of axonogenesis / phosphorylation / RHOV GTPase cycle / branching morphogenesis of an epithelial tube / positive regulation of intracellular estrogen receptor signaling pathway / RHOJ GTPase cycle / stimulatory C-type lectin receptor signaling pathway / RHOQ GTPase cycle / exocytosis / RHO GTPases activate PAKs / Fc-gamma receptor signaling pathway involved in phagocytosis / regulation of MAPK cascade / RHOU GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / Generation of second messenger molecules / positive regulation of JUN kinase activity / Sema3A PAK dependent Axon repulsion / intercalated disc / ephrin receptor signaling pathway / Smooth Muscle Contraction / RAC2 GTPase cycle / RAC3 GTPase cycle / RHO GTPases activate PKNs / positive regulation of peptidyl-serine phosphorylation / collagen binding / positive regulation of stress fiber assembly / ruffle / positive regulation of microtubule polymerization / EPHB-mediated forward signaling / RAC1 GTPase cycle / CD209 (DC-SIGN) signaling / neuron projection morphogenesis / cellular response to starvation / Signal transduction by L1 / VEGFR2 mediated vascular permeability / actin filament / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / wound healing / MAPK6/MAPK4 signaling / Regulation of actin dynamics for phagocytic cup formation / Z disc / ruffle membrane / G beta:gamma signalling through CDC42 / cell-cell junction / cell migration / lamellipodium / positive regulation of protein phosphorylation / chromosome / actin cytoskeleton organization / protein autophosphorylation / nuclear membrane / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / protein phosphorylation / chromatin remodeling / axon / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / centrosome / dendrite / DNA damage response / protein-containing complex / nucleoplasm / ATP binding
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: 1.847 Å
AuthorsDementiev, A. / Suto, R.K. / Olland, A.M.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Identification of a p21-Activated Kinase 1 (PAK1) Inhibitor with 10-fold Selectivity Against PAK2
Authors: Johns, D. / Olejniczak, J. / Babbar, A. / Boone, C. / Cakici, O. / Cheng, M. / Cheng, Q. / Dementiev, A. / Eick, M. / Ferdyan, N. / Fontano, E. / Forman, A. / Goel, V. / Hirst, G. / ...Authors: Johns, D. / Olejniczak, J. / Babbar, A. / Boone, C. / Cakici, O. / Cheng, M. / Cheng, Q. / Dementiev, A. / Eick, M. / Ferdyan, N. / Fontano, E. / Forman, A. / Goel, V. / Hirst, G. / Kozlowski, R. / Lee, S. / Mehta, S. / Mowery, K. / Murray, B. / Nguyen, V. / Olland, A. / Phan, K. / Reich, S. / Rivera, L. / Sabat, M. / Sprengeler, P. / Srinivasan, K. / Sun, Z. / Suto, R. / Wilkinson, T. / Wang, C. / Yu, N. / Xu, M.
History
DepositionAug 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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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)67,3084
Polymers66,3982
Non-polymers9102
Water1,802100
1
A: Serine/threonine-protein kinase PAK 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6542
Polymers33,1991
Non-polymers4551
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)33,6542
Polymers33,1991
Non-polymers4551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.306, 80.946, 65.883
Angle α, β, γ (deg.)90, 106.61, 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 BL21(DE3) (bacteria)
References: UniProt: Q13153, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-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


Mass: 455.019 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27ClN6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Na-malonate buffer, pH 6.8 , 0.15 M DL-malic acid, 4% propanediol, and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.847→60.738 Å / Num. obs: 50948 / % possible obs: 93.2 % / Redundancy: 5.3 % / CC1/2: 0.997 / Net I/σ(I): 10.9
Reflection shellResolution: 1.847→1.879 Å / Num. unique obs: 2730 / CC1/2: 0.603

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.847→60.738 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 9.152 / SU ML: 0.122 / Cross valid method: FREE R-VALUE / ESU R: 0.141 / ESU R Free: 0.134
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2266 2562 5.036 %
Rwork0.1879 48316 -
all0.19 --
obs-50878 93.023 %
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: 58.183 Å2
Baniso -1Baniso -2Baniso -3
1-1.895 Å20 Å22.311 Å2
2---1.047 Å2-0 Å2
3----1.89 Å2
Refinement stepCycle: LAST / Resolution: 1.847→60.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4370 0 62 100 4532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124570
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164382
X-RAY DIFFRACTIONr_angle_refined_deg1.681.8336207
X-RAY DIFFRACTIONr_angle_other_deg0.561.74710122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3815574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.5856.45231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89610791
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.24110185
X-RAY DIFFRACTIONr_chiral_restr0.080.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025306
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02972
X-RAY DIFFRACTIONr_nbd_refined0.2210.21018
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.24133
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22308
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22435
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2156
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2050.24
X-RAY DIFFRACTIONr_nbd_other0.1960.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4380.23
X-RAY DIFFRACTIONr_mcbond_it4.2874.8562287
X-RAY DIFFRACTIONr_mcbond_other4.2844.8562287
X-RAY DIFFRACTIONr_mcangle_it6.0458.6922855
X-RAY DIFFRACTIONr_mcangle_other6.0448.6952856
X-RAY DIFFRACTIONr_scbond_it5.3395.382283
X-RAY DIFFRACTIONr_scbond_other5.3385.3822284
X-RAY DIFFRACTIONr_scangle_it8.2029.6763340
X-RAY DIFFRACTIONr_scangle_other8.2019.6783341
X-RAY DIFFRACTIONr_lrange_it10.51945.9255155
X-RAY DIFFRACTIONr_lrange_other10.51945.9215142
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
1.847-1.8950.341730.32838290.32940290.9150.90699.32990.316
1.895-1.9470.3281130.31524110.31639050.9140.91464.63510.293
1.947-2.0030.292170.26736010.26838260.9330.94399.79090.245
2.003-2.0650.2911770.25728600.25936930.9370.94982.23670.233
2.065-2.1330.2671360.23525120.23736110.9580.96173.33150.212
2.133-2.2070.2571570.20633240.20834830.9570.97199.94260.188
2.207-2.2910.2581370.225160.20333390.9580.97279.45490.177
2.291-2.3840.241760.19230530.19532330.9650.97799.87630.176
2.384-2.490.2571640.19229460.19531140.9630.97999.87150.18
2.49-2.6110.2551600.19727920.229560.9660.97999.86470.191
2.611-2.7520.2491420.19126870.19428370.9670.9899.7180.193
2.752-2.9190.2341160.19525320.19626520.9680.97799.84920.2
2.919-3.120.2711230.19724060.225330.9530.97699.84210.211
3.12-3.3690.2231450.20321890.20523450.9690.97599.53090.219
3.369-3.6890.221150.18720430.18921630.9730.98199.76880.208
3.689-4.1230.183880.16218550.16319520.980.98599.53890.191
4.123-4.7570.157840.13816320.13917270.9840.98999.36310.172
4.757-5.8170.217620.17214040.17414730.9730.98499.52480.229
5.817-8.1890.258550.19510860.19911450.9640.97999.65070.256
8.189-60.7380.163220.1636380.1636640.9830.98499.39760.226
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)
10.543-0.067-0.33810.25930.41061.0283-0.0303-0.0415-0.05340.0195-0.00720.0170.00710.05630.03750.11470.01180.05490.01460.00930.029314.1813-5.465647.8626
20.16310.19850.09550.30380.18940.3226-0.0289-0.00970.00490.0578-0.01390.05630.0650.0050.04280.15080.00620.08150.0088-0.00080.04880.86070.226715.0796
Refinement TLS groupSelection: ALL

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