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- PDB-4o0y: Back pocket flexibility provides group-II PAK selectivity for typ... -

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Basic information

Entry
Database: PDB / ID: 4o0y
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 / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-2OO / Serine/threonine-protein kinase PAK 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,4062
Polymers33,0681
Non-polymers3371
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.988, 63.988, 186.751
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-2OO / 4-[1-(4-amino-1,3,5-triazin-2-yl)-2-(ethylamino)-1H-benzimidazol-6-yl]-2-methylbut-3-yn-2-ol


Mass: 337.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N7O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 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, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2012
RadiationMonochromator: Liquid Nitrogen cooled Dual Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→44.619 Å / Num. all: 20708 / Num. obs: 20439 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.2→2.28 Å / % possible all: 99.8

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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: 2.2→44.619 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1032 5.07 %5% random
Rwork0.198 ---
obs0.2 20369 98.74 %-
all-20708 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 15.449 Å2 / ksol: 0.314 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-16.1785 Å20 Å20 Å2
2--16.1785 Å20 Å2
3---12.3557 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2299 0 25 103 2427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082375
X-RAY DIFFRACTIONf_angle_d1.1183221
X-RAY DIFFRACTIONf_dihedral_angle_d14.019905
X-RAY DIFFRACTIONf_chiral_restr0.079359
X-RAY DIFFRACTIONf_plane_restr0.004414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1978-2.31370.34511420.25742703X-RAY DIFFRACTION100
2.3137-2.45860.321440.23962738X-RAY DIFFRACTION100
2.4586-2.64840.29831500.23322734X-RAY DIFFRACTION100
2.6484-2.91490.25151300.23112755X-RAY DIFFRACTION99
2.9149-3.33660.29231420.21772735X-RAY DIFFRACTION98
3.3366-4.20330.24471550.19372774X-RAY DIFFRACTION98
4.2033-44.62850.17871690.16322898X-RAY DIFFRACTION97
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)
10.15960.1545-0.07730.31860.17610.4016-0.09910.01550.05690.16620.0632-0.1593-0.0391-0.0533-0.01240.19180.0399-0.04570.0815-0.01550.146516.0161-25.673822.968
20.94140.17260.79140.61670.50340.8859-0.23330.19570.1386-0.2330.13410.0297-0.21970.0391-0.13730.193-0.043-0.05520.11380.02470.13625.5055-26.32410.4834
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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