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- PDB-7n91: P70 S6K1 IN COMPLEX WITH MSC2317067A-1 -

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Basic information

Entry
Database: PDB / ID: 7n91
TitleP70 S6K1 IN COMPLEX WITH MSC2317067A-1
ComponentsRibosomal protein S6 kinase beta-1
KeywordsTRANSFERASE/INHIBITOR / Kinase Domain / Inhibitor / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


long-chain fatty acid import into cell / response to electrical stimulus involved in regulation of muscle adaptation / response to methamphetamine hydrochloride / skeletal muscle atrophy / regulation of D-glucose import / positive regulation of skeletal muscle tissue growth / negative regulation of TORC2 signaling / response to L-leucine / cellular response to nutrient / TORC1 signaling ...long-chain fatty acid import into cell / response to electrical stimulus involved in regulation of muscle adaptation / response to methamphetamine hydrochloride / skeletal muscle atrophy / regulation of D-glucose import / positive regulation of skeletal muscle tissue growth / negative regulation of TORC2 signaling / response to L-leucine / cellular response to nutrient / TORC1 signaling / response to glucagon / positive regulation of smooth muscle cell migration / phosphatidylinositol-mediated signaling / response to testosterone / germ cell development / TOR signaling / mTORC1-mediated signalling / positive regulation of translational initiation / response to tumor necrosis factor / long-term memory / behavioral fear response / skeletal muscle contraction / response to glucose / response to mechanical stimulus / positive regulation of TORC1 signaling / negative regulation of insulin receptor signaling pathway / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / peptide binding / protein phosphatase 2A binding / positive regulation of translation / negative regulation of extrinsic apoptotic signaling pathway / PDZ domain binding / positive regulation of smooth muscle cell proliferation / modulation of chemical synaptic transmission / response to nutrient levels / cellular response to growth factor stimulus / cellular response to type II interferon / G1/S transition of mitotic cell cycle / cellular response to insulin stimulus / response to toxic substance / cell migration / peptidyl-serine phosphorylation / response to lipopolysaccharide / response to ethanol / mitochondrial outer membrane / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / postsynapse / protein kinase activity / neuron projection / response to xenobiotic stimulus / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / perinuclear region of cytoplasm / glutamatergic synapse / cell surface / signal transduction / mitochondrion / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S6 kinase / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Ribosomal protein S6 kinase / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1RJ / Ribosomal protein S6 kinase beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsMochalkin, I.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Identification of Clinical Candidate M2698, a Dual p70S6K and Akt Inhibitor, for Treatment of PAM Pathway-Altered Cancers.
Authors: DeSelm, L. / Huck, B. / Lan, R. / Neagu, C. / Potnick, J. / Xiao, Y. / Chen, X. / Jones, R. / Richardson, T.E. / Heasley, B.H. / Haxell, T. / Moore, J. / Tian, H. / Georgi, K. / Rohdich, F. ...Authors: DeSelm, L. / Huck, B. / Lan, R. / Neagu, C. / Potnick, J. / Xiao, Y. / Chen, X. / Jones, R. / Richardson, T.E. / Heasley, B.H. / Haxell, T. / Moore, J. / Tian, H. / Georgi, K. / Rohdich, F. / Sutton, A. / Johnson, T. / Mochalkin, I. / Jackson, J. / Lin, J. / Crowley, L. / Machl, A. / Clark, A. / Wilker, E. / Sherer, B. / Goutopoulos, A.
History
DepositionJun 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Ribosomal protein S6 kinase beta-1
B: Ribosomal protein S6 kinase beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7714
Polymers77,0932
Non-polymers6792
Water00
1
A: Ribosomal protein S6 kinase beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8862
Polymers38,5461
Non-polymers3391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosomal protein S6 kinase beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8862
Polymers38,5461
Non-polymers3391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.300, 74.550, 150.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribosomal protein S6 kinase beta-1 / S6K-beta-1 / S6K1 / 70 kDa ribosomal protein S6 kinase 1 / P70S6K1 / p70-S6K 1 / Ribosomal protein ...S6K-beta-1 / S6K1 / 70 kDa ribosomal protein S6 kinase 1 / P70S6K1 / p70-S6K 1 / Ribosomal protein S6 kinase I / Serine/threonine-protein kinase 14A / p70 ribosomal S6 kinase alpha / p70 S6 kinase alpha / p70 S6K-alpha / p70 S6KA


Mass: 38546.258 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN (81-421) DIGEST / Mutation: T412E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KB1, STK14A / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P23443, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-1RJ / 4-{[(1S)-1-(3-fluorophenyl)-2-(methylamino)ethyl]amino}quinazoline-8-carboxamide


Mass: 339.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18FN5O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2M Bis-Tris pH 5.5, 0.1M Li2SO4, 26-28% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→46.52 Å / Num. obs: 13883 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 5.87 % / Rmerge(I) obs: 0.148 / Rrim(I) all: 0.168 / Net I/σ(I): 11.5
Reflection shellResolution: 3→3.17 Å / Redundancy: 5.49 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.86 / Num. unique obs: 2106 / Rrim(I) all: 0.564 / % possible all: 95.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
CNXrefinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3a60

3a60


Resolution: 3→46.52 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2718 --
Rwork0.2118 --
obs-13883 96.1 %
Displacement parametersBiso max: 97.15 Å2 / Biso mean: 47.7211 Å2 / Biso min: 18.04 Å2
Refinement stepCycle: LAST / Resolution: 3→46.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4976 0 50 0 5026

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