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- PDB-8uwn: Crystal structure of human CLK1 kinase in complex with compound 3 -

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Basic information

Entry
Database: PDB / ID: 8uwn
TitleCrystal structure of human CLK1 kinase in complex with compound 3
ComponentsDual specificity protein kinase CLK1
KeywordsSIGNALING PROTEIN / Kinase / Inhibitor / Transferase
Function / homology
Function and homology information


dual-specificity kinase / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / non-membrane spanning protein tyrosine kinase activity / protein tyrosine kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus
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
: / Dual specificity protein kinase CLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKim, J.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Transl Med / Year: 2024
Title: An ALK2 inhibitor, BLU-782, prevents heterotopic ossification in a mouse model of fibrodysplasia ossificans progressiva.
Authors: Davis, A.J. / Brooijmans, N. / Brubaker, J.D. / Stevison, F. / LaBranche, T.P. / Albayya, F. / Fleming, P. / Hodous, B.L. / Kim, J.L. / Kim, S. / Lobbardi, R. / Palmer, M. / Sheets, M.P. / ...Authors: Davis, A.J. / Brooijmans, N. / Brubaker, J.D. / Stevison, F. / LaBranche, T.P. / Albayya, F. / Fleming, P. / Hodous, B.L. / Kim, J.L. / Kim, S. / Lobbardi, R. / Palmer, M. / Sheets, M.P. / Vassiliadis, J. / Wang, R. / Williams, B.D. / Wilson, D. / Xu, L. / Zhu, X.J. / Bouchard, K. / Hunter, J.W. / Graul, C. / Greenblatt, E. / Hussein, A. / Lyon, M. / Russo, J. / Stewart, R. / Dorsch, M. / Guzi, T.J. / Kadambi, V. / Lengauer, C. / Garner, A.P.
History
DepositionNov 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7403
Polymers42,2131
Non-polymers5272
Water12,034668
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.752, 64.358, 80.822
Angle α, β, γ (deg.)90.00, 119.43, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1526-

HOH

21A-1547-

HOH

31A-1599-

HOH

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Components

#1: Protein Dual specificity protein kinase CLK1


Mass: 42213.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK1 / Production host: Escherichia coli (E. coli) / References: UniProt: P49759
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-XQX / cyclopropyl(4-{(8R)-6-[4-(piperazin-1-yl)phenyl]pyrrolo[1,2-b]pyridazin-4-yl}piperazin-1-yl)methanone


Mass: 430.545 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H30N6O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 301 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.10 M Li2-Sulfate, 0.10 M Tris/HCl, pH 8.8, 15.00 %(w/v) PEG 4000
PH range: 7.5-8.8

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Data collection

DiffractionMean temperature: 101 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.8→29.35 Å / Num. obs: 37677 / % possible obs: 97.9 % / Redundancy: 2.7 % / Rrim(I) all: 0.11 / Net I/σ(I): 10.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.5 % / Num. unique obs: 5437 / Rrim(I) all: 0.62 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.016 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24034 1864 4.9 %RANDOM
Rwork0.17709 ---
obs0.18015 35813 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.899 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å2-0 Å2-0.44 Å2
2--1.12 Å20 Å2
3----0.71 Å2
Refinement stepCycle: 1 / Resolution: 1.8→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2762 0 37 668 3467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192912
X-RAY DIFFRACTIONr_bond_other_d0.0020.022761
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.9673949
X-RAY DIFFRACTIONr_angle_other_deg0.96336363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9575344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.42923.007143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40415513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2011522
X-RAY DIFFRACTIONr_chiral_restr0.0870.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023224
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02707
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6742.4061350
X-RAY DIFFRACTIONr_mcbond_other2.6732.4071351
X-RAY DIFFRACTIONr_mcangle_it3.8673.5981687
X-RAY DIFFRACTIONr_mcangle_other3.8673.5991688
X-RAY DIFFRACTIONr_scbond_it3.5362.8711562
X-RAY DIFFRACTIONr_scbond_other3.5352.8711563
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3594.152255
X-RAY DIFFRACTIONr_long_range_B_refined9.86923.9464155
X-RAY DIFFRACTIONr_long_range_B_other8.8721.3993629
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 146 -
Rwork0.351 2613 -
obs--97.22 %

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