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- PDB-3nax: PDK1 in complex with inhibitor MP7 -

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Basic information

Entry
Database: PDB / ID: 3nax
TitlePDK1 in complex with inhibitor MP7
Components3-phosphoinositide-dependent protein kinase 1
KeywordsTRANSFERASE / Kinase / 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-MP7 / 3-phosphoinositide-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsYan, Y. / Munshi, S.K. / Allison, T.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Genetic and pharmacological inhibition of PDK1 in cancer cells: characterization of a selective allosteric kinase inhibitor.
Authors: Nagashima, K. / Shumway, S.D. / Sathyanarayanan, S. / Chen, A.H. / Dolinski, B. / Xu, Y. / Keilhack, H. / Nguyen, T. / Wiznerowicz, M. / Li, L. / Lutterbach, B.A. / Chi, A. / Paweletz, C. / ...Authors: Nagashima, K. / Shumway, S.D. / Sathyanarayanan, S. / Chen, A.H. / Dolinski, B. / Xu, Y. / Keilhack, H. / Nguyen, T. / Wiznerowicz, M. / Li, L. / Lutterbach, B.A. / Chi, A. / Paweletz, C. / Allison, T. / Yan, Y. / Munshi, S.K. / Klippel, A. / Kraus, M. / Bobkova, E.V. / Deshmukh, S. / Xu, Z. / Mueller, U. / Szewczak, A.A. / Pan, B.S. / Richon, V. / Pollock, R. / Blume-Jensen, P. / Northrup, A. / Andersen, J.N.
History
DepositionJun 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)36,6112
Polymers36,0941
Non-polymers5161
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.668, 44.943, 42.204
Angle α, β, γ (deg.)109.27, 90.50, 62.43
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 36094.465 Da / Num. of mol.: 1 / Fragment: UNP residues 66 to 362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf21
References: UniProt: O15530, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-MP7 / 1-(3,4-difluorobenzyl)-2-oxo-N-{(1R)-2-[(2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)oxy]-1-phenylethyl}-1,2-dihydropyridine-3-carboxamide


Mass: 516.495 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H22F2N4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 1.93 Å3/Da / Density % sol: 36.43 %
Crystal growMethod: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 27466 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 20.02 Å2 / Rsym value: 0.04 / Net I/σ(I): 30
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 7.8 / Num. unique all: 1391 / % possible all: 94

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Processing

Software
NameVersionClassification
StructureStudiodata collection
AMoREphasing
BUSTER2.9.4refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→11.41 Å / Cor.coef. Fo:Fc: 0.9583 / Cor.coef. Fo:Fc free: 0.9432 / SU R Cruickshank DPI: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1339 5.08 %RANDOM
Rwork0.1639 ---
obs0.1655 26354 96.94 %-
Displacement parametersBiso mean: 21.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.2674 Å2-0.2757 Å2-0.3973 Å2
2--0.0252 Å20.1463 Å2
3---0.2422 Å2
Refine analyzeLuzzati coordinate error obs: 0.165 Å
Refinement stepCycle: LAST / Resolution: 1.75→11.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 38 296 2601
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0123632
X-RAY DIFFRACTIONt_angle_deg1.0131872
X-RAY DIFFRACTIONt_dihedral_angle_d8252
X-RAY DIFFRACTIONt_trig_c_planes642
X-RAY DIFFRACTIONt_gen_planes3415
X-RAY DIFFRACTIONt_it236320
X-RAY DIFFRACTIONt_omega_torsion3.27
X-RAY DIFFRACTIONt_other_torsion15.94
X-RAY DIFFRACTIONt_improper_torsion10
X-RAY DIFFRACTIONt_chiral_improper_torsion2955
X-RAY DIFFRACTIONt_ideal_dist_contact29984
LS refinement shellResolution: 1.75→1.82 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2666 144 4.94 %
Rwork0.1941 2772 -
all0.1976 2916 -
obs--96.94 %

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