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- PDB-7b34: MST3 in complex with compound MRIA12 -

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Basic information

Entry
Database: PDB / ID: 7b34
TitleMST3 in complex with compound MRIA12
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 / regulation of axon regeneration / execution phase of apoptosis / intrinsic apoptotic signaling pathway in response to oxidative stress / 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 ...Apoptotic execution phase / regulation of axon regeneration / execution phase of apoptosis / intrinsic apoptotic signaling pathway in response to oxidative stress / 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 / Golgi membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol
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-SQK / Serine/threonine-protein kinase 24
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)35,5059
Polymers34,5601
Non-polymers9458
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint16 kcal/mol
Surface area12820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.262, 59.067, 61.795
Angle α, β, γ (deg.)90.000, 93.050, 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SQK / 8-[(5-azanyl-1,3-dioxan-2-yl)methyl]-6-[2-chloranyl-4-(3-fluoranyl-6-methyl-pyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7-one


Mass: 510.948 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H24ClFN6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.97 Å3/Da / Density % sol: 58.61 %
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: 14% PEG 6000, 0.1M HEPES pH 7.2.

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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→39.73 Å / Num. obs: 20791 / % possible obs: 99.1 % / Redundancy: 5.4 % / Biso Wilson estimate: 37.93 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.042 / Net I/σ(I): 12.1
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1732 / CC1/2: 0.518 / Rpim(I) all: 0.477 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0627refinement
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZHP

3zhp


Resolution: 2.1→39.73 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4887
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2153 1010 4.86 %
Rwork0.1892 19772 -
obs0.1905 20782 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.97 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2052 0 64 66 2182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792157
X-RAY DIFFRACTIONf_angle_d0.91452915
X-RAY DIFFRACTIONf_chiral_restr0.0532327
X-RAY DIFFRACTIONf_plane_restr0.0053397
X-RAY DIFFRACTIONf_dihedral_angle_d3.50881311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.210.30121700.27052818X-RAY DIFFRACTION99.7
2.21-2.350.27791330.24752829X-RAY DIFFRACTION99.73
2.35-2.530.27011610.22622789X-RAY DIFFRACTION99.39
2.53-2.790.26221530.22062804X-RAY DIFFRACTION98.27
2.79-3.190.281370.21382821X-RAY DIFFRACTION98.7
3.19-4.020.22751150.18082862X-RAY DIFFRACTION99.53
4.02-39.730.13921410.14762849X-RAY DIFFRACTION96.98
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)
16.654919291881.59743723095-0.5938947335338.18359813833-0.8591282021866.84778632875-0.4302663975650.4851212540980.0846387121058-0.7385055521620.6340282878440.378714597576-0.164890199835-0.497831500859-0.1682355526170.395205443073-0.0836774905835-0.04505267632670.5145600689710.0002971457070330.366673728861-41.6647354216-9.6601379662912.1375284466
22.814705778561.127318885651.093675527181.81023139851.328969596392.18028815251-0.02683528123080.211685698667-0.236563264889-0.2312827813020.0678150093065-0.1292817078460.0765432333801-0.0698437528255-0.03410573537570.337439271228-0.0225354430590.0356367104690.2685482722790.0059122317490.293697239248-26.9619726597-5.2431804402816.6842172935
32.145771425190.8623439904550.2096549270883.29856910124-0.4670750462872.97423124047-0.06993094595030.0959112234217-0.0349098407085-0.162684476030.0716313969994-0.281082433525-0.09717331620730.1220399897030.007862658844890.223851906094-0.001307786246430.01893423670540.259672004415-0.01246822350330.28104977813-14.59589446696.8538830719721.5338843466
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 172 )
3X-RAY DIFFRACTION3chain 'A' and (resid 173 through 306 )

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