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- PDB-7b30: MST3 in complex with compound G-5555 -

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Basic information

Entry
Database: PDB / ID: 7b30
TitleMST3 in complex with compound G-5555
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 / Apoptotic cleavage of cellular proteins / positive regulation of axon regeneration / negative regulation of cell migration / cellular response to starvation / 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 / Apoptotic cleavage of cellular proteins / positive regulation of axon regeneration / negative regulation of cell migration / cellular response to starvation / cellular response to oxidative stress / protein autophosphorylation / 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 / cadherin binding / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / ATP binding / metal ion binding / nucleus / 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-59T / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,0532
Polymers34,5601
Non-polymers4931
Water1,946108
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 area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.997, 58.846, 61.843
Angle α, β, γ (deg.)90.000, 92.921, 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-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.: 1 / Source method: obtained synthetically / Formula: C25H25ClN6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 52.74 %
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 and 0.5 mM TCEP. Reservoir: 10% 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: 2.1→39.64 Å / Num. obs: 20236 / % possible obs: 97 % / Redundancy: 6 % / Biso Wilson estimate: 38.68 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.03 / Net I/σ(I): 12.6
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1341 / CC1/2: 0.881 / Rpim(I) all: 0.19 / % possible all: 79.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZHP

3zhp


Resolution: 2.1→39.64 Å / SU ML: 0.1967 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5467
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1963 951 4.7 %
Rwork0.1775 19278 -
obs0.1784 20229 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.91 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 35 108 2178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792119
X-RAY DIFFRACTIONf_angle_d1.00462882
X-RAY DIFFRACTIONf_chiral_restr0.0551326
X-RAY DIFFRACTIONf_plane_restr0.0058393
X-RAY DIFFRACTIONf_dihedral_angle_d5.9821309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.210.23211480.20422342X-RAY DIFFRACTION83.45
2.21-2.350.24951230.19692805X-RAY DIFFRACTION99.46
2.35-2.530.20041490.19952796X-RAY DIFFRACTION99.53
2.53-2.790.24831450.20532811X-RAY DIFFRACTION98.83
2.79-3.190.25551370.20412811X-RAY DIFFRACTION99.23
3.19-4.020.21891100.1752842X-RAY DIFFRACTION99.16
4.02-39.640.13871390.15072871X-RAY DIFFRACTION98.01
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)
16.161384958920.0158538985161-4.269616998013.22738199113-2.318820629227.525858131420.001086800227980.4332392882590.040476064644-0.4263452990660.2023021466910.0838960298597-0.0975212301551-0.645617619507-0.1748818068540.403029975266-0.0744936305741-0.06791192131180.479578415894-0.04049028357380.352300686307-39.7322034339-8.418286475189.91675836961
22.938265431981.142213024990.7470915961422.379902539770.6210086706691.96927657434-0.08739953357890.120181216349-0.265794877395-0.1377312187920.121654006037-0.3208289664960.0008576321426680.0344248489246-0.03549029307390.248347064532-0.0004700286709560.01868423016670.250805677524-0.01979930663080.292937005249-19.39016315821.3553807796520.0780001824
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11(chain A and resseq 26:75)26 - 751 - 50
22(chain A and resseq 76:305)76 - 30551 - 263

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