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- PDB-3ion: PDK1 in complex with Compound 8h -

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Basic information

Entry
Database: PDB / ID: 3ion
TitlePDK1 in complex with Compound 8h
Components3-phosphoinositide-dependent protein kinase 1
KeywordsTRANSFERASE / PDK-1 / inhibitor / Alternative splicing / ATP-binding / Cytoplasm / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase
Function / homology
Function and homology information


3-phosphoinositide-dependent protein kinase activity / Activation of AKT2 / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / type B pancreatic cell development / positive regulation of phospholipase activity / hyperosmotic response / RSK activation / regulation of canonical NF-kappaB signal transduction / positive regulation of vascular endothelial cell proliferation ...3-phosphoinositide-dependent protein kinase activity / Activation of AKT2 / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / type B pancreatic cell development / positive regulation of phospholipase activity / hyperosmotic response / RSK activation / regulation of canonical NF-kappaB signal transduction / positive regulation of vascular endothelial cell proliferation / negative regulation of cardiac muscle cell apoptotic process / phospholipase activator activity / positive regulation of sprouting angiogenesis / Constitutive Signaling by AKT1 E17K in Cancer / CD28 dependent PI3K/Akt signaling / phospholipase binding / positive regulation of blood vessel endothelial cell migration / Role of LAT2/NTAL/LAB on calcium mobilization / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Estrogen-stimulated signaling through PRKCZ / negative regulation of endothelial cell apoptotic process / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / GPVI-mediated activation cascade / extrinsic apoptotic signaling pathway / T cell costimulation / cellular response to epidermal growth factor stimulus / activation of protein kinase B activity / Integrin signaling / insulin-like growth factor receptor signaling pathway / positive regulation of release of sequestered calcium ion into cytosol / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / cell projection / peptidyl-threonine phosphorylation / positive regulation of protein localization to plasma membrane / calcium-mediated signaling / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of protein kinase activity / epidermal growth factor receptor signaling pathway / CLEC7A (Dectin-1) signaling / cellular response to insulin stimulus / FCERI mediated NF-kB activation / positive regulation of angiogenesis / G beta:gamma signalling through PI3Kgamma / Regulation of TP53 Degradation / cell migration / Downstream TCR signaling / PIP3 activates AKT signaling / insulin receptor signaling pathway / actin cytoskeleton organization / cytoplasmic vesicle / protein autophosphorylation / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PDK1-type, PH domain / PH domain / PDPK1 family / : / PH-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...PDK1-type, PH domain / PH domain / PDPK1 family / : / PH-like domain superfamily / 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-8H1 / 3-phosphoinositide-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOlland, A.M.
CitationJournal: Eur.J.Med.Chem. / Year: 2010
Title: The identification of 8,9-dimethoxy-5-(2-aminoalkoxy-pyridin-3-yl)-benzo[c][2,7]naphthyridin-4-ylamines as potent inhibitors of 3-phosphoinositide-dependent kinase-1 (PDK-1).
Authors: Nittoli, T. / Dushin, R.G. / Ingalls, C. / Cheung, K. / Floyd, M.B. / Fraser, H. / Olland, A. / Hu, Y. / Grosu, G. / Han, X. / Arndt, K. / Guo, B. / Wissner, A.
History
DepositionAug 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-phosphoinositide-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1503
Polymers35,5731
Non-polymers5782
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.368, 123.368, 47.265
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein 3-phosphoinositide-dependent protein kinase 1 / hPDK1


Mass: 35572.871 Da / Num. of mol.: 1 / Fragment: Protein kinase domain residues 48-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDPK1, PDK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O15530, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-8H1 / 2-(5-{[(2S)-2-amino-3-phenylpropyl]oxy}pyridin-3-yl)-8,9-dimethoxybenzo[c][2,7]naphthyridin-4-amine


Mass: 481.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H27N5O3
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.92 Å3/Da / Density % sol: 57.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: VAPOR DIFFUSION, HANGING DROP, pH 8.6, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Oct 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. obs: 15542

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→26.71 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.884 / SU B: 8.637 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.36 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28179 827 5.1 %RANDOM
Rwork0.24454 ---
obs0.2464 15542 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.831 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20.44 Å20 Å2
2--0.87 Å20 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.4→26.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 41 20 2300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222336
X-RAY DIFFRACTIONr_angle_refined_deg1.0261.9993151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2865272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49623.524105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08315424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.371514
X-RAY DIFFRACTIONr_chiral_restr0.070.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021739
X-RAY DIFFRACTIONr_nbd_refined0.170.2959
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21566
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.267
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.23
X-RAY DIFFRACTIONr_mcbond_it0.4291.51418
X-RAY DIFFRACTIONr_mcangle_it0.76922209
X-RAY DIFFRACTIONr_scbond_it0.77631118
X-RAY DIFFRACTIONr_scangle_it1.3254.5942
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 55 -
Rwork0.341 1140 -
obs--99.92 %

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