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- PDB-7n93: P70 S6K1 IN COMPLEX WITH MSC2363318A-1 -

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Basic information

Entry
Database: PDB / ID: 7n93
TitleP70 S6K1 IN COMPLEX WITH MSC2363318A-1
ComponentsRibosomal protein S6 kinase beta-1Ribosome
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 / skeletal muscle atrophy / positive regulation of skeletal muscle tissue growth / regulation of glucose import / ribosomal protein S6 kinase activity / response to L-leucine / cellular response to nutrient / phosphatidylinositol-mediated signaling / response to glucagon ...long-chain fatty acid import into cell / response to electrical stimulus involved in regulation of muscle adaptation / skeletal muscle atrophy / positive regulation of skeletal muscle tissue growth / regulation of glucose import / ribosomal protein S6 kinase activity / response to L-leucine / cellular response to nutrient / phosphatidylinositol-mediated signaling / response to glucagon / response to testosterone / positive regulation of smooth muscle cell migration / TOR signaling / mTORC1-mediated signalling / germ cell development / positive regulation of translational initiation / skeletal muscle contraction / long-term memory / behavioral fear response / response to tumor necrosis factor / response to glucose / response to mechanical stimulus / negative regulation of insulin receptor signaling pathway / positive regulation of TORC1 signaling / protein serine/threonine/tyrosine kinase activity / cellular response to dexamethasone stimulus / positive regulation of mitotic cell cycle / response to nutrient levels / positive regulation of translation / protein phosphatase 2A binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / PDZ domain binding / negative regulation of extrinsic apoptotic signaling pathway / peptide binding / positive regulation of smooth muscle cell proliferation / G1/S transition of mitotic cell cycle / modulation of chemical synaptic transmission / response to toxic substance / cellular response to growth factor stimulus / cellular response to type II interferon / cellular response to insulin stimulus / cell migration / postsynapse / peptidyl-serine phosphorylation / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / non-specific serine/threonine protein kinase / neuron projection / protein kinase activity / response to xenobiotic stimulus / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / negative regulation of apoptotic process / perinuclear region of cytoplasm / 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. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...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. / 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
Similarity search - Domain/homology
Chem-1SK / Ribosomal protein S6 kinase beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)77,9924
Polymers77,0932
Non-polymers9002
Water724
1
A: Ribosomal protein S6 kinase beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9962
Polymers38,5461
Non-polymers4501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosomal protein S6 kinase beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9962
Polymers38,5461
Non-polymers4501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.020, 75.450, 151.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A84 - 418
2116B84 - 418

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Components

#1: Protein Ribosomal protein S6 kinase beta-1 / Ribosome / 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-1SK / 4-({(1S)-2-(azetidin-1-yl)-1-[4-chloro-3-(trifluoromethyl)phenyl]ethyl}amino)quinazoline-8-carboxamide


Mass: 449.857 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H19ClF3N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.66 %
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: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 6, 2011
RadiationMonochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.739→47.53 Å / Num. obs: 18874 / % possible obs: 98.9 % / Redundancy: 6.27 % / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.076 / Net I/σ(I): 16.64
Reflection shellResolution: 2.739→2.89 Å / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2854 / Rrim(I) all: 0.603 / % possible all: 93.5

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.5.0066refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3a60

3a60


Resolution: 2.74→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.907 / SU B: 38.003 / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.43 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29 941 5 %RANDOM
Rwork0.2115 ---
obs0.2155 17873 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 78.13 Å2 / Biso mean: 50.346 Å2 / Biso min: 21.75 Å2
Refinement stepCycle: final / Resolution: 2.74→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4972 0 62 4 5038
Biso mean--60.59 29.13 -
Num. residues----621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225179
X-RAY DIFFRACTIONr_angle_refined_deg1.2081.9956992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5935621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24223.853231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.14115.016936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5781532
X-RAY DIFFRACTIONr_chiral_restr0.0710.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213872
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2431 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.545
LOOSE THERMAL1.6810
LS refinement shellResolution: 2.74→2.809 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.418 58 -
Rwork0.299 1112 -
obs--100 %

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