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- PDB-7cmb: Crystal Structure of PAK4 in complex with inhibitor 41 -

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Basic information

Entry
Database: PDB / ID: 7cmb
TitleCrystal Structure of PAK4 in complex with inhibitor 41
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 / 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
Chem-G5X / Serine/threonine-protein kinase PAK 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.592 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
DepositionJul 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)33,4742
Polymers33,0981
Non-polymers3751
Water724
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)64.522, 64.522, 176.901
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: 33098.449 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-G5X / 1-(2-azanylpyrimidin-4-yl)-6-[2-(1-oxidanylcyclohexyl)ethynyl]indole-3-carboxamide


Mass: 375.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.78 Å3/Da / Density % sol: 55.78 % / Mosaicity: 1.254 ° / Mosaicity esd: 0.019 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5
Details: 0.2M Ammonium sulfate, 0.1M Tris pH 8.5, 25% PEG3350

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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 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.592→50 Å / Num. obs: 12343 / % possible obs: 99.9 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.053 / Rrim(I) all: 0.155 / Χ2: 1.926 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.648.91.0855820.9390.3691.1470.533100
2.64-2.698.60.9976330.8940.3441.0570.701100
2.69-2.748.40.6495670.9650.2280.6880.586100
2.74-2.88.50.6366010.9540.2230.6750.575100
2.8-2.868.80.6516100.9450.2260.690.601100
2.86-2.939.50.5685980.960.1870.5990.65100
2.93-39.50.4845900.9670.1610.5110.74499.8
3-3.089.30.3926310.9690.130.4140.92100
3.08-3.179.40.3265840.9840.1090.3441.086100
3.17-3.289.30.2776140.9810.0920.2931.24100
3.28-3.399.20.2566060.9890.0870.2711.534100
3.39-3.538.60.2286080.9890.080.2422.10499.8
3.53-3.698.10.186120.9910.0660.1922.656100
3.69-3.888.70.1626100.9940.0570.1723.122100
3.88-4.138.70.1466210.9940.0510.1553.634100
4.13-4.458.10.1186240.9940.0430.1263.9399.7
4.45-4.897.60.1076270.9930.0410.1153.99799.8
4.89-5.67.10.1066330.9920.0420.1153.84699.2
5.6-7.058.20.0936610.9950.0330.0993.474100
7.05-506.10.0727310.9960.0310.0793.92999.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data scaling
PHENIX1.14_3247refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XVF

5xvf


Resolution: 2.592→26.063 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2509 621 5.08 %
Rwork0.2059 11605 -
obs0.2081 12226 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.78 Å2 / Biso mean: 75.003 Å2 / Biso min: 39.97 Å2
Refinement stepCycle: final / Resolution: 2.592→26.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 28 4 2333
Biso mean--59.41 67.22 -
Num. residues----291
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5922-2.85280.331540.2547281099
2.8528-3.26490.28581470.24262856100
3.2649-4.11080.23721580.21672881100
4.1108-26.0630.23751620.1855305899

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