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- PDB-6b16: P21-activated kinase 1 in complex with a 4-azaindole inhibitor -

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Basic information

Entry
Database: PDB / ID: 6b16
TitleP21-activated kinase 1 in complex with a 4-azaindole inhibitor
ComponentsSerine/threonine-protein kinase PAK 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase / inhibitor / Complex / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of cell proliferation involved in contact inhibition / protein localization to cytoplasmic stress granule / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / RHO GTPases Activate ROCKs / gamma-tubulin binding / Activation of RAC1 / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of intracellular estrogen receptor signaling pathway ...negative regulation of cell proliferation involved in contact inhibition / protein localization to cytoplasmic stress granule / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / RHO GTPases Activate ROCKs / gamma-tubulin binding / Activation of RAC1 / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of intracellular estrogen receptor signaling pathway / DSCAM interactions / RHOV GTPase cycle / regulation of axonogenesis / branching morphogenesis of an epithelial tube / Fc-gamma receptor signaling pathway involved in phagocytosis / RHOJ GTPase cycle / RHOQ GTPase cycle / exocytosis / RHO GTPases activate PAKs / stimulatory C-type lectin receptor signaling pathway / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle / Sema3A PAK dependent Axon repulsion / Generation of second messenger molecules / intercalated disc / Smooth Muscle Contraction / RAC3 GTPase cycle / RAC2 GTPase cycle / ephrin receptor signaling pathway / localization / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / positive regulation of JUN kinase activity / positive regulation of stress fiber assembly / ruffle / RAC1 GTPase cycle / EPHB-mediated forward signaling / collagen binding / CD209 (DC-SIGN) signaling / neuron projection morphogenesis / VEGFR2 mediated vascular permeability / Signal transduction by L1 / actin filament / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / MAPK6/MAPK4 signaling / wound healing / G beta:gamma signalling through CDC42 / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / Z disc / cell-cell junction / cell migration / lamellipodium / positive regulation of peptidyl-serine phosphorylation / chromosome / actin cytoskeleton organization / nuclear membrane / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of cell migration / intracellular signal transduction / chromatin remodeling / positive regulation of protein phosphorylation / axon / phosphorylation / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / dendrite / apoptotic process / DNA damage response / positive regulation of cell population proliferation / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / plasma membrane / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic 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-C7Y / Serine/threonine-protein kinase PAK 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.285 Å
AuthorsRouge, L. / Wang, W.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2016
Title: Synthesis and evaluation of a series of 4-azaindole-containing p21-activated kinase-1 inhibitors.
Authors: Lee, W. / Crawford, J.J. / Aliagas, I. / Murray, L.J. / Tay, S. / Wang, W. / Heise, C.E. / Hoeflich, K.P. / La, H. / Mathieu, S. / Mintzer, R. / Ramaswamy, S. / Rouge, L. / Rudolph, J.
History
DepositionSep 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PAK 1
B: Serine/threonine-protein kinase PAK 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9645
Polymers67,1472
Non-polymers8173
Water82946
1
A: Serine/threonine-protein kinase PAK 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0303
Polymers33,5741
Non-polymers4562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase PAK 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9342
Polymers33,5741
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.682, 82.458, 66.036
Angle α, β, γ (deg.)90.00, 106.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase PAK 1 / Alpha-PAK / p21-activated kinase 1 / PAK-1 / p65-PAK


Mass: 33573.547 Da / Num. of mol.: 2 / Fragment: UNP residues 249-545
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13153, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-C7Y / N~4~-(5-cyclopropyl-1H-pyrazol-3-yl)-N~2~-[(1S)-1-(1H-pyrrolo[3,2-b]pyridin-5-yl)ethyl]pyrimidine-2,4-diamine


Mass: 360.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20N8
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 25% PEG 3500, 0.2M Ammonium Sulfate and 0.1M Tris pH 8

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.285→50 Å / Num. obs: 29195 / % possible obs: 99.9 % / Redundancy: 3.8 % / Net I/σ(I): 24.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.285→38.558 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.53
RfactorNum. reflection% reflection
Rfree0.2496 1484 5.09 %
Rwork0.2015 --
obs0.2039 29153 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.285→38.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4410 0 59 46 4515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044548
X-RAY DIFFRACTIONf_angle_d0.8496152
X-RAY DIFFRACTIONf_dihedral_angle_d13.0791717
X-RAY DIFFRACTIONf_chiral_restr0.029705
X-RAY DIFFRACTIONf_plane_restr0.004783
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2851-2.35890.32571290.26872390X-RAY DIFFRACTION94
2.3589-2.44320.29181340.26072501X-RAY DIFFRACTION100
2.4432-2.5410.31891460.25512507X-RAY DIFFRACTION100
2.541-2.65660.31111230.24172534X-RAY DIFFRACTION100
2.6566-2.79660.28721570.23322464X-RAY DIFFRACTION100
2.7966-2.97180.28351200.22912562X-RAY DIFFRACTION100
2.9718-3.20110.2731170.22522529X-RAY DIFFRACTION100
3.2011-3.52310.29391450.22532527X-RAY DIFFRACTION100
3.5231-4.03240.23441550.19252523X-RAY DIFFRACTION100
4.0324-5.07860.21681050.17612567X-RAY DIFFRACTION100
5.0786-38.56310.21821530.1732565X-RAY DIFFRACTION99
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)
10.19310.3949-0.35640.8978-0.19860.3513-0.54910.0941-0.4362-0.12970.1407-0.1987-0.061-0.1914-0.0180.47090.06950.02830.7496-0.26820.815922.1038-22.01047.7078
21.7531-0.0278-0.23341.34960.24262.4069-0.09770.0957-0.15080.07080.1079-0.0112-0.11430.4567-00.39580.0365-0.0240.5305-0.00710.374124.4682-0.221321.2228
30.64120.11810.18110.13130.22720.53680.0290.24730.0330.5898-0.41370.13410.2988-0.1727-0.05760.8562-0.10850.10570.307-0.02020.579-2.0406-16.1755-15.1319
40.96580.2049-0.2591-0.1167-0.6352.1338-0.0341-0.34360.0388-0.07260.03610.1735-0.06380.1007-0.0060.41490.03620.01970.4355-0.02730.445715.32544.7822-16.6742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 249:346
2X-RAY DIFFRACTION2chain A and resid 347:541 or chain L and resid 1
3X-RAY DIFFRACTION3chain B and resid 249:346
4X-RAY DIFFRACTION4chain B and resid 347:541 or chain L and resid 2

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