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- PDB-3nay: PDK1 in complex with inhibitor MP6 -

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Basic information

Entry
Database: PDB / ID: 3nay
TitlePDK1 in complex with inhibitor MP6
Components3-phosphoinositide-dependent protein kinase 1
KeywordsTRANSFERASE / Kinase / Serine/threonine protein kinase
Function / homology
Function and homology information


intracellular signaling cassette / Activation of AKT2 / regulation of mast cell degranulation / type B pancreatic cell development / negative regulation of toll-like receptor signaling pathway / RSK activation / regulation of canonical NF-kappaB signal transduction / hyperosmotic response / positive regulation of vascular endothelial cell proliferation / negative regulation of cardiac muscle cell apoptotic process ...intracellular signaling cassette / Activation of AKT2 / regulation of mast cell degranulation / type B pancreatic cell development / negative regulation of toll-like receptor signaling pathway / RSK activation / regulation of canonical NF-kappaB signal transduction / hyperosmotic response / 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 / positive regulation of blood vessel endothelial cell migration / Role of LAT2/NTAL/LAB on calcium mobilization / negative regulation of endothelial cell apoptotic process / Estrogen-stimulated signaling through PRKCZ / vascular endothelial cell response to laminar fluid shear stress / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / phospholipase binding / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / GPVI-mediated activation cascade / RHO GTPases activate PKNs / T cell costimulation / extrinsic apoptotic signaling pathway / Integrin signaling / insulin-like growth factor receptor signaling pathway / cellular response to epidermal growth factor stimulus / positive regulation of release of sequestered calcium ion into cytosol / VEGFR2 mediated cell proliferation / 3-phosphoinositide-dependent protein kinase activity / VEGFR2 mediated vascular permeability / cell projection / positive regulation of protein localization to plasma membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of transforming growth factor beta receptor signaling pathway / calcium-mediated signaling / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / epidermal growth factor receptor signaling pathway / cellular response to insulin stimulus / positive regulation of angiogenesis / Regulation of TP53 Degradation / Downstream TCR signaling / G beta:gamma signalling through PI3Kgamma / insulin receptor signaling pathway / cell migration / PIP3 activates AKT signaling / protein autophosphorylation / actin cytoskeleton organization / cytoplasmic vesicle / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / postsynaptic density / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site ...PDK1-type, PH domain / PH domain / PDPK1 family / : / PH-like domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-MP6 / 3-phosphoinositide-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsYan, Y. / Munshi, S.K. / Allison, T.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Selective inhibition of PDK1 using an allosteric kinase inhibitor and RNAi impairs cancer cell migration and anchorage-independent growth of primary tumor lines
Authors: Nagashima, K. / Shumway, S.D. / Sathyanarayanan, S. / Chen, A. / Dolinski, B. / Xu, Y. / Keilhack, H. / Nguyen, T. / Wiznerowicz, M. / Li, L. / Lutterbach, B.A. / Paweletz, C. / Allison, T. ...Authors: Nagashima, K. / Shumway, S.D. / Sathyanarayanan, S. / Chen, A. / Dolinski, B. / Xu, Y. / Keilhack, H. / Nguyen, T. / Wiznerowicz, M. / Li, L. / Lutterbach, B.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 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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
B: 3-phosphoinositide-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2044
Polymers72,3492
Non-polymers8552
Water2,684149
1
A: 3-phosphoinositide-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6022
Polymers36,1741
Non-polymers4281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3-phosphoinositide-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6022
Polymers36,1741
Non-polymers4281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.677, 89.677, 178.000
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 3-phosphoinositide-dependent protein kinase 1 / hPDK1


Mass: 36174.441 Da / Num. of mol.: 2 / Fragment: UNP residues 66 to 362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDPK1, PDK1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf21
References: UniProt: O15530, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-MP6 / 4-(2-cyclopropylethylidene)-9-(1H-pyrazol-4-yl)-6-{[(1R)-1,2,2-trimethylpropyl]amino}benzo[c][1,6]naphthyridin-1(4H)-one


Mass: 427.541 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H29N5O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING 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: Feb 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 23041 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 66.89 Å2 / Rsym value: 0.098 / Net I/σ(I): 21
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 2260 / % possible all: 97.6

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Processing

Software
NameVersionClassification
StructureStudiodata collection
CNSrefinement
BUSTER2.9.4refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→44.84 Å / Cor.coef. Fo:Fc: 0.9324 / Cor.coef. Fo:Fc free: 0.8889 / SU R Cruickshank DPI: 0.593 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2738 1181 5.14 %RANDOM
Rwork0.2081 ---
obs0.2114 22984 99.47 %-
Displacement parametersBiso mean: 53.32 Å2
Baniso -1Baniso -2Baniso -3
1--5.2802 Å20 Å20 Å2
2---5.2802 Å20 Å2
3---10.5603 Å2
Refine analyzeLuzzati coordinate error obs: 0.378 Å
Refinement stepCycle: LAST / Resolution: 2.6→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4544 0 64 149 4757
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00947262
X-RAY DIFFRACTIONt_angle_deg1.1563922
X-RAY DIFFRACTIONt_dihedral_angle_d16282
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes1202
X-RAY DIFFRACTIONt_gen_planes6785
X-RAY DIFFRACTIONt_it472620
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.62
X-RAY DIFFRACTIONt_other_torsion19.97
X-RAY DIFFRACTIONt_improper_torsion60
X-RAY DIFFRACTIONt_chiral_improper_torsion5905
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact53614
LS refinement shellResolution: 2.6→2.71 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3057 142 5.3 %
Rwork0.2972 2537 -
all0.2977 2679 -
obs--99.47 %

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