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- PDB-7b35: MST3 in complex with compound MRIA13 -

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Basic information

Entry
Database: PDB / ID: 7b35
TitleMST3 in complex with compound MRIA13
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 / negative regulation of cell migration / cellular response to starvation / protein autophosphorylation / 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 / negative regulation of cell migration / cellular response to starvation / protein autophosphorylation / cellular response to oxidative stress / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / cadherin binding / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / ATP binding / metal ion binding / nucleus / membrane / 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-SQB / Serine/threonine-protein kinase 24
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.40005138292 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
B: Serine/threonine-protein kinase 24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1654
Polymers69,1192
Non-polymers1,0462
Water88349
1
A: Serine/threonine-protein kinase 24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0832
Polymers34,5601
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase 24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0832
Polymers34,5601
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.875, 93.210, 61.303
Angle α, β, γ (deg.)90.000, 92.191, 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 24 / Mammalian STE20-like protein kinase 3 / MST-3 / STE20-like kinase MST3


Mass: 34559.648 Da / Num. of mol.: 2
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-SQB / 8-[(5-azanyl-1,3-dioxan-2-yl)methyl]-6-[2-chloranyl-4-(3-methoxy-6-methyl-pyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7-one


Mass: 522.983 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H27ClN6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.67 Å3/Da / Density % sol: 54 %
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: 24% PEG 3550, 0.1M citrate pH 5.6.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / 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: 2.4→47.9 Å / Num. obs: 24436 / % possible obs: 99.2 % / Redundancy: 5.6 % / Biso Wilson estimate: 37.6372586557 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.059 / Net I/σ(I): 9.2
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2563 / CC1/2: 0.823 / Rpim(I) all: 0.353 / % possible all: 99.1

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Processing

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

3zhp


Resolution: 2.40005138292→47.8982003597 Å / SU ML: 0.318970742139 / Cross valid method: FREE R-VALUE / σ(F): 1.34879973523 / Phase error: 29.572755986
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.26347576468 1199 4.91353167773 %
Rwork0.205015470048 23203 -
obs0.20779101366 24402 99.0381103129 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.3716855479 Å2
Refinement stepCycle: LAST / Resolution: 2.40005138292→47.8982003597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4009 0 74 49 4132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003678624303564179
X-RAY DIFFRACTIONf_angle_d0.667355038495699
X-RAY DIFFRACTIONf_chiral_restr0.0454355038966652
X-RAY DIFFRACTIONf_plane_restr0.00540035337559780
X-RAY DIFFRACTIONf_dihedral_angle_d15.21348042972535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.49610.3376474292231480.2681223396772530X-RAY DIFFRACTION99.0018484288
2.4961-2.60970.3215524718111400.2686252863512503X-RAY DIFFRACTION96.9196919692
2.6097-2.74730.3144300939441300.2570356970962582X-RAY DIFFRACTION98.9781021898
2.7473-2.91940.2951631655941290.2495761839062605X-RAY DIFFRACTION99.890390939
2.9194-3.14480.375725263951170.2377178716962578X-RAY DIFFRACTION99.6303142329
3.1448-3.46120.3135534848071380.2262660702992594X-RAY DIFFRACTION99.6353026988
3.4612-3.96180.2293188646371300.1917394921472592X-RAY DIFFRACTION99.743495786
3.9618-4.99060.2111896098761220.1630254600712582X-RAY DIFFRACTION98.1132075472
4.9906-47.89820035970.2108828402491450.1725832135192637X-RAY DIFFRACTION99.4992846924
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)
17.811461656830.1696472594642.625470689076.18461101567-1.081602106728.977583055410.8348325223350.2072786135540.02053345491510.522126887153-0.0379175157208-0.331349451448-0.783542220924-0.130745097-0.678519018120.7511496736280.004414017444750.1234741847230.2894761934640.003587015761770.450705751310.258303865539.72231816113.4351313816
21.49115043888-0.8848651793480.7259917575893.33963296737-1.94253135652.39685063182-0.0838917857120.0394647277118-0.02070896136250.3100300520260.1625770731430.244752846775-0.303936120247-0.0330985990191-0.05983833022550.547862976953-0.0006598362007610.0939742528930.242710956445-0.02222730252310.35066492514211.862518638825.493418642717.1551601065
32.28797599468-0.84587158211-0.8990590326612.699014407710.1413658186182.00410663134-0.0310043554714-0.134508785023-0.03922470405660.2473102228660.1042975876870.0564755789208-0.02562513611880.132517626624-0.08458912014640.540772701841-0.006636477627120.03825409884660.260957857383-0.002925349893910.29984309933223.396146811711.351934389521.3058283296
43.99151885193-0.4244547014561.354138742553.532089502860.9673179947428.272684093760.0619169064082-0.236579848103-0.0563285801451-0.210860667308-0.0294731790166-0.2907002956730.4291967504140.122302045847-0.1487686799350.537768627359-0.005323156253450.1062711301640.267563321449-0.01692094044510.46442015466236.73934584657.3073353543552.7155104889
51.185410490040.891890602423-0.8167235659832.99197319116-1.435707984872.69051970747-0.08264811808810.0554613920854-0.0880079328672-0.175404889985-0.001686185804590.08374096626050.315728968667-0.1197970827470.09854072194450.493558593850.03848771401790.04559798393730.242460731316-0.03362118359550.34241458656739.131200178721.694243320144.7875781492
66.724969758763.61965963826-0.6204282797042.62471761469-1.129902833311.502236560320.122310072612-0.727370798788-0.03653054100050.343036601961-0.1319599309720.283959194618-0.2203275628860.1210722234540.03113126669610.6751381903350.04086539068650.07409668527590.4378955450140.03276371060740.3277989460147.284437278432.911343619653.3055188783
72.191093634160.2964050840661.060967096931.132928130770.7474045692912.525364038930.04343429819120.08469271779830.203290409372-0.124828272738-0.03427175420670.0130228736129-0.1949977349660.17878082348-0.009400156805730.5650164372010.0302417622950.1047026588410.253222303270.02074361667760.31859673902251.00263868434.41992865739.5583041543
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 55 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 172 )
3X-RAY DIFFRACTION3chain 'A' and (resid 173 through 304 )
4X-RAY DIFFRACTION4chain 'B' and (resid 26 through 75 )
5X-RAY DIFFRACTION5chain 'B' and (resid 76 through 172 )
6X-RAY DIFFRACTION6chain 'B' and (resid 173 through 209 )
7X-RAY DIFFRACTION7chain 'B' and (resid 210 through 304 )

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