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- PDB-7cp4: Crystal Structure of PAK4 in complex with inhibitor 55 -

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Basic information

Entry
Database: PDB / ID: 7cp4
TitleCrystal Structure of PAK4 in complex with inhibitor 55
ComponentsSerine/threonine-protein kinase PAK 4
KeywordsTRANSFERASE / ATP binding pocket
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 / regulation of MAPK cascade / RHOQ GTPase cycle / cellular response to organic cyclic compound / 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 / regulation of MAPK cascade / RHOQ GTPase cycle / cellular response to organic cyclic compound / 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 / regulation of cell growth / adherens junction / 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 / 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
Chem-GCC / Serine/threonine-protein kinase PAK 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhao, F. / Li, H.
CitationJournal: to be published
Title: Discovery of 6-ethynyl-1H-indole-3-carboxamide Derivatives as Highly Potent and Selective p21-Activated Kinase 4 (PAK4) Inhibitors
Authors: Song, P. / Zhao, F. / Cheng, M.
History
DepositionAug 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)33,4702
Polymers33,0111
Non-polymers4591
Water90150
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)63.917, 80.364, 54.611
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-748-

HOH

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Components

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


Mass: 33011.371 Da / Num. of mol.: 1 / Fragment: Protein kinase domain
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-GCC / [1-(2-azanylpyrimidin-4-yl)-6-[2-(1-oxidanylcyclohexyl)ethynyl]indol-3-yl]-[(3S)-3-methylpiperazin-1-yl]methanone


Mass: 458.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H30N6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.2M Ammonium sulfate, 0.1M Bis-tris 5.5, 25% PEG 3350, 0.1M Guanidine hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.466→50 Å / Num. obs: 10540 / % possible obs: 99.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.073 / Rrim(I) all: 0.172 / Χ2: 2.279 / Net I/σ(I): 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.545.90.4554980.8540.2080.5021.201100
2.54-2.596.10.465320.8530.2070.5061.226100
2.59-2.645.90.4325080.8850.1980.4771.227100
2.64-2.6960.4165080.8930.1880.4581.368100
2.69-2.755.80.3765280.9030.1710.4151.525100
2.75-2.825.50.355200.8870.1650.3881.594100
2.82-2.895.70.3185150.9330.1450.3511.64100
2.89-2.966.20.3155290.9540.140.3451.6599.8
2.96-3.056.20.265260.9360.1170.2861.859100
3.05-3.156.20.2375110.9580.1050.262.005100
3.15-3.266.10.2135370.9720.0950.2342.36799.6
3.26-3.3960.1895180.970.0850.2082.54100
3.39-3.555.70.1775200.9820.0830.1962.65299.8
3.55-3.735.10.165220.9780.0790.1792.935100
3.73-3.975.60.1365390.9830.0650.1513.25999.6
3.97-4.275.60.1145320.9860.0540.1273.28898.3
4.27-4.75.50.1025230.990.0490.1143.29797.4
4.7-5.385.10.15290.9850.050.1123.24898.9
5.38-6.785.50.1085560.9850.050.1193.40999.6
6.78-504.40.0815890.9930.0450.0934.01997.2

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Processing

Software
NameVersionClassification
PHENIX1.14_3247refinement
DENZOdata reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J0I

2j0i


Resolution: 2.5→41.52 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2517 528 5.03 %
Rwork0.1961 9969 -
obs0.1989 10497 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.45 Å2 / Biso mean: 35.9057 Å2 / Biso min: 16.56 Å2
Refinement stepCycle: final / Resolution: 2.5→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2307 0 34 50 2391
Biso mean--35.64 37.75 -
Num. residues----292
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.71440.29091310.2202240998
2.7144-3.10710.30661260.22392479100
3.1071-3.91410.22881390.19532495100
3.9141-41.520.23561320.1797258698

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