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- PDB-7b31: MST3 in complex with compound MRIA9 -

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Basic information

Entry
Database: PDB / ID: 7b31
TitleMST3 in complex with compound MRIA9
ComponentsSerine/threonine-protein kinase 24
KeywordsTRANSFERASE / kinase inhibitors / structure-based drug design / SIK2 inhibitor / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Apoptotic execution phase / FAR/SIN/STRIPAK complex / regulation of axon regeneration / intrinsic apoptotic signaling pathway in response to oxidative stress / execution phase of apoptosis / positive regulation of axon regeneration / Apoptotic cleavage of cellular proteins / cellular response to starvation / negative regulation of cell migration / cellular response to oxidative stress ...Apoptotic execution phase / FAR/SIN/STRIPAK complex / regulation of axon regeneration / intrinsic apoptotic signaling pathway in response to oxidative stress / execution phase of apoptosis / positive regulation of axon regeneration / Apoptotic cleavage of cellular proteins / cellular response to starvation / negative regulation of cell migration / cellular response to oxidative stress / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / protein phosphorylation / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation domain / : / 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-SQ8 / Serine/threonine-protein kinase 24
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTesch, R. / Rak, M. / Joerger, A.C. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)397659447 Germany
CitationJournal: J.Med.Chem. / Year: 2021
Title: Structure-Based Design of Selective Salt-Inducible Kinase Inhibitors.
Authors: Tesch, R. / Rak, M. / Raab, M. / Berger, L.M. / Kronenberger, T. / Joerger, A.C. / Berger, B.T. / Abdi, I. / Hanke, T. / Poso, A. / Strebhardt, K. / Sanhaji, M. / Knapp, S.
History
DepositionNov 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase 24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0562
Polymers34,5601
Non-polymers4961
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.429, 59.068, 61.728
Angle α, β, γ (deg.)90.000, 93.517, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Serine/threonine-protein kinase 24 / Mammalian STE20-like protein kinase 3 / MST-3 / STE20-like kinase MST3


Mass: 34559.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK24, MST3, STK3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y6E0, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-SQ8 / 1-[(5-azanyl-1,3-dioxan-2-yl)methyl]-3-[2-chloranyl-4-(3-fluoranylpyridin-2-yl)phenyl]-7-(methylamino)-1,6-naphthyridin-2-one


Mass: 495.933 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C25H23ClFN5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein solution: 10 mg/ml in buffer 25 mM HEPES pH 7.5, 200 mM NaCl, 5% glycerol, 0.5 mM TCEP. Reservoir: 16% PEG 6000, 0.1M HEPES pH 7.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00004 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.8→39.86 Å / Num. obs: 33013 / % possible obs: 99.4 % / Redundancy: 6.1 % / Biso Wilson estimate: 29.53 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1926 / CC1/2: 0.742 / Rpim(I) all: 0.352 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.15.2_3472refinement
Aimlessdata scaling
XDSdata processing
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZHP

3zhp


Resolution: 1.8→39.86 Å / SU ML: 0.1749 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.471
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2121 1590 4.82 %
Rwork0.1769 31418 -
obs0.1785 33008 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.82 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2060 0 35 128 2223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642149
X-RAY DIFFRACTIONf_angle_d0.81382919
X-RAY DIFFRACTIONf_chiral_restr0.0527329
X-RAY DIFFRACTIONf_plane_restr0.0052397
X-RAY DIFFRACTIONf_dihedral_angle_d2.49331811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.2431240.22322865X-RAY DIFFRACTION99.47
1.86-1.920.24981550.2142835X-RAY DIFFRACTION99.57
1.92-20.24711370.19882859X-RAY DIFFRACTION99.5
2-2.090.2521360.1912813X-RAY DIFFRACTION99.49
2.09-2.20.18411530.1862875X-RAY DIFFRACTION99.74
2.2-2.340.23461560.18892823X-RAY DIFFRACTION98.97
2.34-2.520.21761470.1972814X-RAY DIFFRACTION98.37
2.52-2.780.22321430.1972869X-RAY DIFFRACTION99.87
2.78-3.180.2221640.20012879X-RAY DIFFRACTION99.71
3.18-40.1991550.16952844X-RAY DIFFRACTION99.4
4-39.860.18971200.14252942X-RAY DIFFRACTION98.39
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.14732196321-0.166383588528-1.887270531073.67810030581-0.9997867818726.66763516987-0.1215413850250.393590819917-0.0109337113065-0.5459887000790.289156901889-0.03857996172520.0454499087931-0.342875896726-0.1385219093570.304186457383-0.0816410272161-0.0371950617810.369362716349-0.01273697987890.296821387169-41.8772728123-9.9253275300412.1254915449
22.344870468941.147239969920.7704519975791.850364967490.7670531713351.50219191408-0.07962023726120.290931724599-0.15022486755-0.2443091513880.107009097821-0.1083883030330.0720208920861-0.0138292371534-0.02644210958310.245614605539-0.01519555591660.01383930390620.210969190791-0.008921868153970.232179430834-25.3364920774-3.9464137328915.2234901797
31.867416598090.549384012182-0.09130044883742.54592026675-0.6045706472843.13391590761-0.03673275498680.0467716936204-0.0008999583994980.001065800224750.0234627305271-0.156971939388-0.08171532400530.003756793689660.01283894674570.178606717735-0.0201115930619-0.02168445606790.187272076822-0.01466777499870.226408502172-14.61313511057.404265421924.0180045613
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 60 )
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 209 )
3X-RAY DIFFRACTION3chain 'A' and (resid 210 through 306 )

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