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- PDB-7zkx: SRPK2 IN COMPLEX WITH INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 7zkx
TitleSRPK2 IN COMPLEX WITH INHIBITOR
ComponentsSRSF protein kinase 2
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / SRPK2 / NUCLEAR PROTEIN
Function / homology
Function and homology information


nuclear speck organization / R-loop processing / regulation of mRNA processing / regulation of mRNA splicing, via spliceosome / Maturation of nucleoprotein / negative regulation of viral genome replication / spliceosomal complex assembly / positive regulation of viral genome replication / positive regulation of cell cycle / 14-3-3 protein binding ...nuclear speck organization / R-loop processing / regulation of mRNA processing / regulation of mRNA splicing, via spliceosome / Maturation of nucleoprotein / negative regulation of viral genome replication / spliceosomal complex assembly / positive regulation of viral genome replication / positive regulation of cell cycle / 14-3-3 protein binding / RNA splicing / positive regulation of neuron apoptotic process / peptidyl-serine phosphorylation / angiogenesis / cell differentiation / non-specific serine/threonine protein kinase / intracellular signal transduction / nuclear speck / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / positive regulation of gene expression / chromatin / nucleolus / magnesium ion binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
ACETATE ION / Chem-IXQ / NITRATE ION / SRSF protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.06 Å
AuthorsGraedler, U.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: MSC-1186, a Highly Selective Pan-SRPK Inhibitor Based on an Exceptionally Decorated Benzimidazole-Pyrimidine Core.
Authors: Schroder, M. / Leiendecker, M. / Gradler, U. / Braun, J. / Blum, A. / Wanior, M. / Berger, B.T. / Kramer, A. / Muller, S. / Esdar, C. / Knapp, S. / Heinrich, T.
History
DepositionApr 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SRSF protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,51813
Polymers70,2071
Non-polymers1,31112
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-47 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.755, 107.755, 90.228
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SRSF protein kinase 2 / SFRS protein kinase 2 / Serine/arginine-rich protein-specific kinase 2 / SR-protein-specific kinase 2


Mass: 70206.562 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRPK2 / Production host: Escherichia coli (E. coli)
References: UniProt: P78362, non-specific serine/threonine protein kinase

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Non-polymers , 6 types, 145 molecules

#2: Chemical ChemComp-IXQ / N-[3-[[[2-(6-chloranyl-5-fluoranyl-1H-benzimidazol-2-yl)pyrimidin-4-yl]amino]methyl]pyridin-2-yl]-N-methyl-methanesulfonamide / N-(3-{[2-(5-Chloro-6-fluoro-1H-benzoimidazol-2-yl)-pyrimidin-4-ylamino]-methyl}-pyridin-2-yl)-N-methyl-methanesulfonamide


Mass: 461.900 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17ClFN7O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.66 Å3/Da / Density % sol: 66.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 5 mM HEPES pH 7.5, 150 mM NaCl, 20 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99989 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99989 Å / Relative weight: 1
ReflectionResolution: 2.06→93.32 Å / Num. obs: 36972 / % possible obs: 97.9 % / Redundancy: 2.9 % / Rrim(I) all: 0.05 / Rsym value: 0.041 / Net I/σ(I): 15.51
Reflection shellResolution: 2.06→2.31 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.53 / Num. unique obs: 10714 / Rrim(I) all: 0.584 / Rsym value: 0.473 / % possible all: 98.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X7G

2x7g


Resolution: 2.06→93.32 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 7.792 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 1766 4.8 %RANDOM
Rwork0.1793 ---
obs0.1807 35191 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 129.33 Å2 / Biso mean: 57.306 Å2 / Biso min: 27.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.13 Å20 Å2
2--0.27 Å2-0 Å2
3----0.87 Å2
Refinement stepCycle: final / Resolution: 2.06→93.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2762 0 80 133 2975
Biso mean--70.13 54.14 -
Num. residues----339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192882
X-RAY DIFFRACTIONr_bond_other_d0.0040.022695
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9653907
X-RAY DIFFRACTIONr_angle_other_deg1.24836177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5045343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71323.492126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10815473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7121516
X-RAY DIFFRACTIONr_chiral_restr0.090.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213195
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02669
LS refinement shellResolution: 2.06→2.114 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 128 -
Rwork0.305 2588 -
all-2716 -
obs--99.23 %

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