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- PDB-9d53: PAK4 in complex with compound 7 -

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Basic information

Entry
Database: PDB / ID: 9d53
TitlePAK4 in complex with compound 7
ComponentsSerine/threonine-protein kinase PAK 4
KeywordsTRANSFERASE / 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 / RHOU GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle ...dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / negative regulation of endothelial cell apoptotic process / RAC1 GTPase cycle / cytoskeleton organization / cellular response to starvation / adherens junction / regulation of cell growth / positive regulation of angiogenesis / cell migration / 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 / 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 / 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: 2.468 Å
AuthorsBoone, C.D. / Olland, A.M. / Suto, R.K.
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,4432
Polymers33,0981
Non-polymers3441
Water905
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)62.703, 62.703, 149.792
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-A1A2P / N~2~-{[(1s,4s)-4-aminocyclohexyl]methyl}-N~4~-(5-cyclopropyl-1,3-thiazol-2-yl)pyrimidine-2,4-diamine


Mass: 344.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H24N6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris-Propane, pH 9.0, 10% PEG 20,000

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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 PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.468→50 Å / Num. obs: 11390 / % possible obs: 99.9 % / Redundancy: 15.9 % / CC1/2: 0.91 / Net I/σ(I): 13.07
Reflection shellResolution: 2.468→2.62 Å / Mean I/σ(I) obs: 1.45 / Num. unique obs: 1783 / CC1/2: 0.91

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.468→48.124 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.938 / SU B: 29.884 / SU ML: 0.287 / Cross valid method: FREE R-VALUE / ESU R: 0.588 / ESU R Free: 0.307
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2627 554 4.898 %
Rwork0.1858 10757 -
all0.19 --
obs-11311 99.298 %
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: 70.605 Å2
Baniso -1Baniso -2Baniso -3
1-1.806 Å2-0 Å2-0 Å2
2--1.806 Å2-0 Å2
3----3.613 Å2
Refinement stepCycle: LAST / Resolution: 2.468→48.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 0 24 5 2322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122368
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162312
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.8433214
X-RAY DIFFRACTIONr_angle_other_deg0.5461.7555327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9165291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.9416.225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97510413
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.86310100
X-RAY DIFFRACTIONr_chiral_restr0.0760.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022761
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02519
X-RAY DIFFRACTIONr_nbd_refined0.2360.2510
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.22260
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21160
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21282
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other00.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.211
X-RAY DIFFRACTIONr_nbd_other0.2090.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0970.22
X-RAY DIFFRACTIONr_mcbond_it5.0275.6141167
X-RAY DIFFRACTIONr_mcbond_other5.0115.6131167
X-RAY DIFFRACTIONr_mcangle_it7.11510.0911457
X-RAY DIFFRACTIONr_mcangle_other7.11210.0911458
X-RAY DIFFRACTIONr_scbond_it5.9276.2091201
X-RAY DIFFRACTIONr_scbond_other5.9276.2121202
X-RAY DIFFRACTIONr_scangle_it8.73311.1521754
X-RAY DIFFRACTIONr_scangle_other8.7311.1541755
X-RAY DIFFRACTIONr_lrange_it10.55954.1992592
X-RAY DIFFRACTIONr_lrange_other10.55754.1922593
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
2.468-2.5310.361430.357620.3518160.8850.90798.6520.361
2.531-2.6010.401490.3077350.3137930.90.93198.86510.309
2.601-2.6760.304350.2927230.2937710.940.95198.31390.292
2.676-2.7580.365430.2647050.2697600.9160.95798.42110.261
2.758-2.8480.331450.2456870.257390.9270.95999.05280.241
2.848-2.9480.346230.2516700.2557020.9180.95898.71790.239
2.948-3.0580.409290.2256540.2316910.8770.96598.84230.215
3.058-3.1830.356330.2236310.2296680.9050.96499.40120.215
3.183-3.3240.283320.2015970.2066310.9460.97399.6830.193
3.324-3.4850.244360.1895870.1926230.9590.9771000.183
3.485-3.6730.224160.1665640.1685820.9720.98499.65640.166
3.673-3.8940.242300.1675250.1715550.9640.9841000.165
3.894-4.1610.246230.1715060.1745300.9580.98199.81130.173
4.161-4.4910.256200.1474740.1514940.9630.9871000.154
4.491-4.9160.244200.1434370.1484580.9480.98699.78170.151
4.916-5.4890.271240.1863950.1914190.970.9771000.198
5.489-6.3240.261190.1973680.2013870.9660.9771000.21
6.324-7.7120.217130.1723140.1743270.9690.9841000.188
7.712-10.770.166110.1152580.1182690.9830.9911000.134
10.77-48.1240.206100.2021650.2021750.9810.9771000.217
Refinement TLS params.Method: refined / Origin x: -20.2058 Å / Origin y: 14.4958 Å / Origin z: 2.9312 Å
111213212223313233
T0.1564 Å20.0692 Å2-0.0249 Å2-0.1419 Å2-0.0147 Å2--0.0179 Å2
L0.1285 °20.2048 °20.3291 °2-0.605 °20.2774 °2--1.1457 °2
S-0.054 Å °-0.0425 Å °0.0001 Å °-0.1224 Å °-0.0183 Å °-0.0523 Å °-0.1916 Å °-0.1191 Å °0.0723 Å °
Refinement TLS groupSelection: ALL

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