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- PDB-7b36: MST4 in complex with compound G-5555 -

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Basic information

Entry
Database: PDB / ID: 7b36
TitleMST4 in complex with compound G-5555
ComponentsSerine/threonine-protein kinase 26
KeywordsTRANSFERASE / kinase inhibitors / Structure-based drug design / SIK2 inhibitor / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


microvillus assembly / FAR/SIN/STRIPAK complex / vesicle membrane / Golgi-associated vesicle / Apoptotic cleavage of cellular proteins / negative regulation of cell migration / cellular response to starvation / cell periphery / cellular response to oxidative stress / protein autophosphorylation ...microvillus assembly / FAR/SIN/STRIPAK complex / vesicle membrane / Golgi-associated vesicle / Apoptotic cleavage of cellular proteins / negative regulation of cell migration / cellular response to starvation / cell periphery / cellular response to oxidative stress / protein autophosphorylation / regulation of apoptotic process / 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 / protein kinase activity / intracellular signal transduction / protein phosphorylation / apical plasma membrane / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / perinuclear region of cytoplasm / magnesium ion binding / Golgi apparatus / protein homodimerization activity / extracellular exosome / ATP binding / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
MST4, kinase domain / 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. ...MST4, kinase domain / 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-59T / Serine/threonine-protein kinase 26
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.10681078505 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 26
C: Serine/threonine-protein kinase 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9298
Polymers67,7222
Non-polymers1,2086
Water1,49583
1
A: Serine/threonine-protein kinase 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5135
Polymers33,8611
Non-polymers6534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Serine/threonine-protein kinase 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4163
Polymers33,8611
Non-polymers5552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.749, 53.186, 93.518
Angle α, β, γ (deg.)90.000, 96.355, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Serine/threonine-protein kinase 26 / MST3 and SOK1-related kinase / Mammalian STE20-like protein kinase 4 / STE20-like kinase MST4 / ...MST3 and SOK1-related kinase / Mammalian STE20-like protein kinase 4 / STE20-like kinase MST4 / Serine/threonine-protein kinase MASK


Mass: 33860.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK26, MASK, MST4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9P289, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-59T / 8-[(trans-5-amino-1,3-dioxan-2-yl)methyl]-6-[2-chloro-4-(6-methylpyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one


Mass: 492.957 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C25H25ClN6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: solution: protein 12 mg/ml in buffer 25mM HEPES pH 7.5, 200 mM NaCl, 0.5mM TCEP, 5% glycerol reservoir: 28% PEG6000, 0.1M HEPES pH 7.5

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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: 2.1→46.48 Å / Num. obs: 35855 / % possible obs: 98.7 % / Redundancy: 5 % / Biso Wilson estimate: 37.7410049082 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.029 / Net I/σ(I): 13.3
Reflection shellResolution: 2.11→2.17 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2756 / CC1/2: 0.886 / Rpim(I) all: 0.348 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZHP

3zhp


Resolution: 2.10681078505→46.4716734331 Å / SU ML: 0.307824106377 / Cross valid method: FREE R-VALUE / σ(F): 1.33493055704 / Phase error: 32.92135848
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.244487399643 1710 4.78294920564 %
Rwork0.200976456902 34042 -
obs0.203059982941 35752 98.387363091 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.0893235375 Å2
Refinement stepCycle: LAST / Resolution: 2.10681078505→46.4716734331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4157 0 83 83 4323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007603059336184329
X-RAY DIFFRACTIONf_angle_d0.8516978573255852
X-RAY DIFFRACTIONf_chiral_restr0.0506070646084646
X-RAY DIFFRACTIONf_plane_restr0.00591640489072799
X-RAY DIFFRACTIONf_dihedral_angle_d14.44896397272626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.16880.4045811905751370.3189519979042683X-RAY DIFFRACTION94.0940940941
2.1688-2.23880.3314518346641460.2566027232132824X-RAY DIFFRACTION98.703888335
2.2388-2.31880.3136677913381560.2401701496962805X-RAY DIFFRACTION98.7
2.3188-2.41170.3115964119741390.2403050245032840X-RAY DIFFRACTION99.0688393748
2.4117-2.52140.3021372716611470.2346387520562839X-RAY DIFFRACTION98.8741721854
2.5214-2.65430.2885161148891580.223110745462841X-RAY DIFFRACTION99.5683930943
2.6543-2.82060.3221973528671420.2238949695242834X-RAY DIFFRACTION99.1008991009
2.8206-3.03840.3156120745561260.2320198605312803X-RAY DIFFRACTION96.7305151915
3.0384-3.3440.2558431524471270.2302859205622894X-RAY DIFFRACTION99.375
3.344-3.82770.2436385496971240.1919473435632885X-RAY DIFFRACTION99.3069306931
3.8277-4.82170.1905505195851550.1593389351262876X-RAY DIFFRACTION99.2144026187
4.8217-46.470.1863062629891530.1720393632152918X-RAY DIFFRACTION97.9585326954
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)
19.70659189894-1.330335844630.9306720848345.81715300623-0.11844998735.17668814245-0.354745879405-0.07469114844740.207867997593-0.395255915650.3899456858050.2387665553550.124403048413-0.543527526129-0.007461978715050.343209378045-0.1351242709330.02426617338650.5159380678010.006886664824020.2981972581836.049743825332.8125285935362.9750985574
21.34604448959-0.120570681286-0.4522781874691.22820314111-1.546042775043.32132658997-0.2546807962150.0865975550432-0.085998789403-0.806431443730.2054094032220.1926453422140.751540150784-0.6794144677630.04771469154250.476662957547-0.130190764632-0.02681429443570.417965517655-0.06139014274770.37311437342512.34431104765.3775823105647.3610598012
30.9866758869510.116823689434-1.298487272625.12547823234-2.955648631253.479035513120.01589819845530.436036057415-0.177844499894-0.549461189839-0.01882989363830.9562654626720.344318226998-1.42053234165-0.0670680212140.4596688682590.00330500960813-0.1397183494490.826222517116-0.09733534050560.5467166060264.435564625414.925939630836.3287298503
42.30419854957-0.07399083038060.7497068900622.83753098736-1.12474035524.94588141951-0.0846063030936-0.002531473763910.0646519232667-0.364545963865-0.00550055827848-0.107681217539-0.0445615761646-0.4340917024050.105641350570.349096535199-0.00582692418120.02524771958650.320313935483-0.02664794057120.31011704419319.970050846817.365496607737.6783626666
56.876168282831.32900478635-0.8433571976924.71344806860.9198638397443.52689061172-0.2138400611220.163156607787-0.05889191453580.1389934185180.2012790913550.415759357101-0.308730929392-0.794263144503-0.01404850875290.3510236421740.1572353631050.05427418637880.6575089190950.05686152977780.3494907398479.830272043616.83568451938-15.9277519341
61.132219186320.009201854414680.2248268589162.13182520373-1.595221867313.69126769878-0.1340111237620.03232082475690.1679447187550.7585144398910.1743247500680.126165297146-0.898904335297-0.685019822088-0.0193329924960.5196258174150.1477742136440.05017810528080.373177373058-0.03019044651880.35801927026217.78128215354.82069083551-0.568655491495
70.07033654882310.167597599635-0.1516230980452.77785923091-3.06839521893.39829558812-0.0385699342261-0.1867805207450.1154586620310.3848944987680.1556067419080.758013078285-0.398475698117-0.697987764382-0.03244961856110.5217676471050.0984460128360.1046147019840.662003303637-0.048747070040.4545722856539.36863774568-5.36895439479.78278052744
81.83283934271-0.187236234435-1.199212922512.82216400772-1.442582759524.71030668011-0.176083797105-0.0209513361308-0.04668937558130.426102254372-0.0496183373552-0.0337227404767-0.136456284083-0.2846222247320.2142798747350.384346129398-0.0107350352864-0.005497466191250.237712060441-0.04506567549050.33322711882324.9070891792-7.314349805028.77684996383
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 60 )
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 160 )
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 197 )
4X-RAY DIFFRACTION4chain 'A' and (resid 198 through 300 )
5X-RAY DIFFRACTION5chain 'C' and (resid 17 through 63 )
6X-RAY DIFFRACTION6chain 'C' and (resid 64 through 160 )
7X-RAY DIFFRACTION7chain 'C' and (resid 161 through 197 )
8X-RAY DIFFRACTION8chain 'C' and (resid 198 through 299 )

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