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- PDB-7cp3: Crystal Structure of PAK4 in complex with inhibitor 47 -

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Basic information

Entry
Database: PDB / ID: 7cp3
TitleCrystal Structure of PAK4 in complex with inhibitor 47
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 / RHOQ GTPase cycle / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU 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 / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle / RHOG GTPase cycle / cellular response to organic cyclic compound / 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 / cell cycle / phosphorylation / focal adhesion / protein serine kinase activity / 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. / Protein kinase domain profile. ...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-GC6 / Serine/threonine-protein kinase PAK 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 5, 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
Water0
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)64.253, 64.253, 185.074
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 33011.371 Da / Num. of mol.: 1 / Fragment: PAK4 Kinase Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK4, KIAA1142 / Plasmid: pSUMOH10 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O96013, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-GC6 / [(3R)-3-azanylpiperidin-1-yl]-[1-(2-azanylpyrimidin-4-yl)-6-[2-(1-oxidanylcyclohexyl)ethynyl]indol-3-yl]methanone


Mass: 458.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H30N6O2 / Feature type: SUBJECT OF INVESTIGATION
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: 2.84 Å3/Da / Density % sol: 56.66 % / Mosaicity: 0.738 ° / Mosaicity esd: 0.018 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5 / Details: 0.1M Tris pH 8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2019 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.899→50 Å / Num. obs: 9172 / % possible obs: 99.2 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.051 / Rrim(I) all: 0.157 / Χ2: 1.872 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.95101.2254360.8440.3991.290.488100
2.95-3100.8094500.8790.2660.8540.537100
3-3.069.70.744600.8810.2450.7810.579100
3.06-3.129.80.6144330.9180.2040.6480.57799.8
3.12-3.199.50.5464560.9380.1830.5770.66399.8
3.19-3.2790.4394460.9440.1510.4660.788100
3.27-3.359.90.3494480.9740.1150.3680.78100
3.35-3.44100.3594430.9190.1190.3791.27399.6
3.44-3.54100.294480.9810.0960.3071.21199.8
3.54-3.65100.2314440.9870.0770.2441.53999.6
3.65-3.789.40.1934710.9880.0660.2051.76499.6
3.78-3.949.40.1844380.990.0630.1952.36899.3
3.94-4.118.80.1474680.9930.0520.1562.29499.4
4.11-4.339.10.1214570.9940.0420.1282.83998.9
4.33-4.69.10.1074550.9950.0370.1133.21999.3
4.6-4.9690.14660.9950.0360.1063.21599.4
4.96-5.468.90.1094590.9940.0390.1173.30498.7
5.46-6.2490.1064740.9940.0360.1123.29598.5
6.24-7.8690.0814910.9960.0280.0873.32498.6
7.86-507.30.0655290.9970.0240.074.09295

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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: 2.9→44.5 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2667 453 4.95 %
Rwork0.2444 8690 -
obs0.2455 9143 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.14 Å2 / Biso mean: 94.0323 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.9→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 34 0 2329
Biso mean--80.31 --
Num. residues----290
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9-3.31790.35171620.3397277199
3.3179-4.17970.31251430.26782888100
4.1797-44.50.21881480.2075303199

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