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- PDB-7zks: SRPK1 IN COMPLEX WITH INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 7zks
TitleSRPK1 IN COMPLEX WITH INHIBITOR
ComponentsSRSF protein kinase 1
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / SRPK1 / NUCLEAR PROTEIN
Function / homology
Function and homology information


sperm DNA condensation / 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 / Replacement of protamines by nucleosomes in the male pronucleus / RNA splicing / chromosome segregation ...sperm DNA condensation / 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 / Replacement of protamines by nucleosomes in the male pronucleus / RNA splicing / chromosome segregation / nuclear matrix / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / nuclear speck / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / chromatin / magnesium ion binding / endoplasmic reticulum / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
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
Chem-IXQ / SRSF protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5833
Polymers44,0851
Non-polymers4972
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-12 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.877, 74.877, 309.168
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 44085.406 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN,KINASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRPK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96SB4, non-specific serine/threonine protein kinase
#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-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 5 mM HEPES pH 7.4, 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: 2.28→64.85 Å / Num. obs: 23552 / % possible obs: 95.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 53.917 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.059 / Rsym value: 0.053 / Χ2: 0.971 / Net I/σ(I): 19.84
Reflection shellResolution: 2.28→2.53 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.52 / Num. unique obs: 6045 / CC1/2: 1 / Rrim(I) all: 0.586 / Rsym value: 0.526 / % possible all: 94.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5xv7

5xv7


Resolution: 2.28→25.31 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.896 / SU R Cruickshank DPI: 0.288 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.315 / SU Rfree Blow DPI: 0.247 / SU Rfree Cruickshank DPI: 0.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2897 1258 5.34 %RANDOM
Rwork0.2428 ---
obs0.2455 23537 96 %-
Displacement parametersBiso max: 108.97 Å2 / Biso mean: 52.35 Å2 / Biso min: 18.9 Å2
Baniso -1Baniso -2Baniso -3
1--6.0496 Å20 Å20 Å2
2---6.0496 Å20 Å2
3---12.0991 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: final / Resolution: 2.28→25.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 32 168 3030
Biso mean--50.15 51.01 -
Num. residues----348
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1024SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes483HARMONIC5
X-RAY DIFFRACTIONt_it2934HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion370SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2277SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2934HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg3977HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion17.53
LS refinement shellResolution: 2.28→2.3 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.451 23 4.88 %
Rwork0.3469 448 -
all0.351 471 -
obs--92.02 %

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