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- PDB-4o0v: Back pocket flexibility provides group-II PAK selectivity for typ... -

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Basic information

Entry
Database: PDB / ID: 4o0v
TitleBack pocket flexibility provides group-II PAK selectivity for type 1 kinase inhibitors
ComponentsSerine/threonine-protein kinase PAK 4
Keywordstransferase/transferase inhibitor / PAK4 / transferase-transferase inhibitor complex
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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-2OL / Serine/threonine-protein kinase PAK 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRouge, L. / Tam, C. / Wang, W.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Back Pocket Flexibility Provides Group II p21-Activated Kinase (PAK) Selectivity for Type I 1/2 Kinase Inhibitors.
Authors: Staben, S.T. / Feng, J.A. / Lyle, K. / Belvin, M. / Boggs, J. / Burch, J.D. / Chua, C.C. / Cui, H. / Dipasquale, A.G. / Friedman, L.S. / Heise, C. / Koeppen, H. / Kotey, A. / Mintzer, R. / ...Authors: Staben, S.T. / Feng, J.A. / Lyle, K. / Belvin, M. / Boggs, J. / Burch, J.D. / Chua, C.C. / Cui, H. / Dipasquale, A.G. / Friedman, L.S. / Heise, C. / Koeppen, H. / Kotey, A. / Mintzer, R. / Oh, A. / Roberts, D.A. / Rouge, L. / Rudolph, J. / Tam, C. / Wang, W. / Xiao, Y. / Young, A. / Zhang, Y. / Hoeflich, K.P.
History
DepositionDec 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references

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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)33,4752
Polymers33,0681
Non-polymers4061
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.473, 65.473, 180.532
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 33068.422 Da / Num. of mol.: 1 / Fragment: unp residues 300-591
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-2OL / 1-({1-(2-aminopyrimidin-4-yl)-2-[(2-methoxyethyl)amino]-1H-benzimidazol-6-yl}ethynyl)cyclohexanol


Mass: 406.481 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26N6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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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: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 500 uL of 0.2 M Tri-Potassium citrate and 20% PEG3350 in the reservoir, and drops set up by mixing 1.0 uL of reservoir solution and 1.0 uL of protein, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2011
RadiationMonochromator: Liquid Nitrogen cooled Dual Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 10316 / Num. obs: 9235 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.8→2.9 Å / % possible all: 97.6

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→44.845 Å / SU ML: 0.48 / σ(F): 1.35 / Phase error: 25.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2531 470 4.74 %
Rwork0.2014 --
obs0.2038 9782 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.023 Å2 / ksol: 0.312 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.3629 Å20 Å2-0 Å2
2--9.3629 Å2-0 Å2
3----27.3105 Å2
Refinement stepCycle: LAST / Resolution: 2.8→44.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 0 30 10 2333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032375
X-RAY DIFFRACTIONf_angle_d0.7533221
X-RAY DIFFRACTIONf_dihedral_angle_d11.605902
X-RAY DIFFRACTIONf_chiral_restr0.054360
X-RAY DIFFRACTIONf_plane_restr0.004413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8004-3.20550.35731690.28863062X-RAY DIFFRACTION97
3.2055-4.03820.27181570.19953137X-RAY DIFFRACTION97
4.0382-44.8510.22031440.18533253X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.69570.0834-0.09350.3175-0.11970.784-0.13210.00260.2644-0.00110.02080.23320.16040.3073-0.0910.24120.15320.05510.97450.05980.568-29.604716.5046-22.2012
21.03381.2907-0.72271.6781-1.15271.54820.36890.03510.04040.276-0.5854-0.02930.09050.5044-0.11980.57290.07740.00290.78180.18570.5618-29.393.0453-1.2173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 299:398 )A299 - 398
2X-RAY DIFFRACTION2( CHAIN A AND RESID 399:589 )A399 - 589

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