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- PDB-9d52: Structure of PAK4 in complex with compound 18 -

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Basic information

Entry
Database: PDB / ID: 9d52
TitleStructure of PAK4 in complex with compound 18
ComponentsSerine/threonine-protein kinase PAK 4
KeywordsTRANSFERASE / Serine/threonine-protein kinase / inhibitor
Function / homology
Function and homology information


dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / : / regulation of MAPK cascade / RHOU GTPase cycle / CDC42 GTPase cycle ...dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / : / regulation of MAPK cascade / RHOU GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / negative regulation of endothelial cell apoptotic process / cytoskeleton organization / RAC1 GTPase cycle / cellular response to starvation / adherens junction / regulation of cell growth / positive regulation of angiogenesis / cell migration / 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 / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / apoptotic process / Golgi apparatus / signal transduction / ATP binding / cytosol / cytoplasm
Similarity search - Function
p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Protein kinase 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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.449 Å
AuthorsBoone, C. / Suto, R. / Olland, A.
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

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6665
Polymers33,0981
Non-polymers5684
Water75742
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.642, 62.642, 184.886
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Serine/threonine-protein kinase PAK 4 / p21-activated kinase 4 / PAK-4


Mass: 33098.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK4, KIAA1142 / Production host: Escherichia coli (E. coli)
References: UniProt: O96013, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1A2R / 2-cyano-N-[3-({6-[(5-cyclopropyl-1,3-thiazol-2-yl)amino]pyrazin-2-yl}amino)bicyclo[1.1.1]pentan-1-yl]acetamide


Mass: 381.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19N7OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 4% (v/v) PEG 8000

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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: Dec 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.449→44.334 Å / Num. obs: 14318 / % possible obs: 99.4 % / Redundancy: 9.7 % / CC1/2: 0.999 / Net I/σ(I): 13.1
Reflection shellResolution: 2.449→2.46 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2259 / CC1/2: 0.515

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.449→44.334 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.9 / SU B: 23.667 / SU ML: 0.253 / Cross valid method: FREE R-VALUE / ESU R: 0.383 / ESU R Free: 0.3
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2872 720 5.038 %
Rwork0.201 13571 -
all0.205 --
obs-14291 99.714 %
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: 70.203 Å2
Baniso -1Baniso -2Baniso -3
1-0.253 Å2-0 Å20 Å2
2--0.253 Å2-0 Å2
3----0.506 Å2
Refinement stepCycle: LAST / Resolution: 2.449→44.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2289 0 39 42 2370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122383
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162338
X-RAY DIFFRACTIONr_angle_refined_deg2.5141.853231
X-RAY DIFFRACTIONr_angle_other_deg0.7951.7585388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9715291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.0366.34626
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.35910421
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.11310101
X-RAY DIFFRACTIONr_chiral_restr0.1160.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022761
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02519
X-RAY DIFFRACTIONr_nbd_refined0.2380.2523
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2170.22295
X-RAY DIFFRACTIONr_nbtor_refined0.190.21131
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.21345
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0860.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0760.27
X-RAY DIFFRACTIONr_nbd_other0.2520.253
X-RAY DIFFRACTIONr_mcbond_it6.0314.8151161
X-RAY DIFFRACTIONr_mcbond_other6.0224.8161161
X-RAY DIFFRACTIONr_mcangle_it7.7688.6571450
X-RAY DIFFRACTIONr_mcangle_other7.7668.6591451
X-RAY DIFFRACTIONr_scbond_it6.695.1761222
X-RAY DIFFRACTIONr_scbond_other6.6885.1791223
X-RAY DIFFRACTIONr_scangle_it8.9199.3381772
X-RAY DIFFRACTIONr_scangle_other8.9169.3391773
X-RAY DIFFRACTIONr_lrange_it10.53945.742595
X-RAY DIFFRACTIONr_lrange_other10.5445.7492596
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
2.449-2.5120.428400.3119950.31510390.8770.92399.6150.31
2.512-2.5810.402640.2929270.2999910.9270.9411000.291
2.581-2.6560.444550.2959190.3039740.9090.9441000.291
2.656-2.7370.394450.2919040.2969500.8830.94699.89470.275
2.737-2.8260.323470.2598760.2629240.9370.95499.89180.242
2.826-2.9250.371400.2668370.278790.9260.95899.77250.245
2.925-3.0350.368440.2288270.2348740.9210.96899.65670.208
3.035-3.1580.284470.2217930.2258430.9410.96799.64410.202
3.158-3.2980.275320.2157750.2178080.9520.97399.87620.203
3.298-3.4580.298340.2257280.2287620.9430.9751000.216
3.458-3.6440.344340.2237040.2287400.9410.97499.72970.215
3.644-3.8630.311340.26640.2057000.940.97799.71430.199
3.863-4.1280.267330.1786350.1826680.9570.9811000.178
4.128-4.4550.303280.1555960.1616280.9490.98599.36310.162
4.455-4.8760.204270.1355450.1385730.9820.98899.82550.145
4.876-5.4430.181270.1434980.1455260.9820.98999.80990.154
5.443-6.2690.249280.1654560.1694860.970.98599.58850.178
6.269-7.640.255250.1763760.1814030.9580.97999.50370.195
7.64-10.6480.208180.1643180.1663400.9690.98198.82350.19
10.648-44.3340.374180.3271990.3312220.8250.92297.74770.342
Refinement TLS params.Method: refined / Origin x: -22.3605 Å / Origin y: 11.3976 Å / Origin z: -7.0363 Å
111213212223313233
T0.0311 Å20.0316 Å20.0051 Å2-0.0956 Å2-0.056 Å2--0.1651 Å2
L1.6669 °20.0466 °2-0.8291 °2-1.2361 °2-0.4423 °2--4.6404 °2
S0.0858 Å °-0.114 Å °0.0019 Å °0.063 Å °-0.0403 Å °0.0572 Å °-0.0107 Å °0.2355 Å °-0.0455 Å °
Refinement TLS groupSelection: ALL

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