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- PDB-6yta: CLK1 bound with imidazopyridazine (Cpd 1) -

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Basic information

Entry
Database: PDB / ID: 6yta
TitleCLK1 bound with imidazopyridazine (Cpd 1)
ComponentsDual specificity protein kinase CLK1
KeywordsTRANSFERASE / Inhibitor / Complex / CLK1 / Structural Genomics / Structural Genomics Consortium / SGC
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
: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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. ...: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-IYZ / Dual specificity protein kinase CLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSchroeder, M. / Chaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2020
Title: DFG-1 Residue Controls Inhibitor Binding Mode and Affinity, Providing a Basis for Rational Design of Kinase Inhibitor Selectivity.
Authors: Schroder, M. / Bullock, A.N. / Fedorov, O. / Bracher, F. / Chaikuad, A. / Knapp, S.
History
DepositionApr 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 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: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9503
Polymers39,5821
Non-polymers3682
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-6 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.378, 64.560, 72.519
Angle α, β, γ (deg.)90.000, 117.550, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Dual specificity protein kinase CLK1 / CDC-like kinase 1


Mass: 39581.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK1, CLK / Production host: Escherichia coli (E. coli) / References: UniProt: P49759, dual-specificity kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-IYZ / 1-(3-{6-[(CYCLOPROPYLMETHYL)AMINO]IMIDAZO[1,2-B]PYRIDAZIN-3-YL}PHENYL)ETHANONE / IMIDAZOPYRIDAZIN 1


Mass: 306.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N4O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 14% PEG 6k, 0.1M bicine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→64.3 Å / Num. obs: 16584 / % possible obs: 99.2 % / Redundancy: 5.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.026 / Rrim(I) all: 0.061 / Net I/σ(I): 20.6 / Num. measured all: 86772 / Scaling rejects: 681
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.385.30.15847016010.9820.070.16510.698.7
8.91-64.35.60.022172030910.010.02439.798.9

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1z57

1z57


Resolution: 2.3→64.3 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.847 / SU B: 13.205 / SU ML: 0.177 / SU R Cruickshank DPI: 0.3896 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.39 / ESU R Free: 0.281
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2752 833 5 %RANDOM
Rwork0.1896 ---
obs0.1938 15708 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 66.7 Å2 / Biso mean: 21.79 Å2 / Biso min: 7.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0 Å20.51 Å2
2---0.25 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.3→64.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 27 216 2943
Biso mean--24.36 26.31 -
Num. residues----338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132817
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172535
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.6363823
X-RAY DIFFRACTIONr_angle_other_deg1.3671.5855873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3995341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32122.466146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55815468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2021514
X-RAY DIFFRACTIONr_chiral_restr0.0920.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023251
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02607
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 57 -
Rwork0.209 1155 -
all-1212 -
obs--98.54 %
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)
11.3106-0.524-0.07335.76622.24132.01120.14410.33920.0868-0.5728-0.19360.2673-0.5064-0.21670.04950.14050.08470.00380.1344-0.00220.0808-0.084315.39121.4679
21.2502-0.2775-0.45341.40080.1330.8929-0.0037-0.08040.05560.0036-0.03390.0332-0.1030.06760.03760.07770.0186-0.0170.0354-0.00370.009915.1347.567821.0741
30.51830.28620.9780.4216-0.33744.8091-0.28430.18990.2292-0.19660.19020.2306-0.49060.03370.09410.2836-0.0349-0.14040.17840.09630.159321.75982.6045-0.9769
42.95030.89610.82022.557-0.43152.9679-0.19240.13330.0268-0.1573-0.0202-0.3338-0.11150.38610.21260.08740.03820.00580.1126-0.00180.088131.59740.98188.6275
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A146 - 209
2X-RAY DIFFRACTION2A210 - 336
3X-RAY DIFFRACTION3A337 - 418
4X-RAY DIFFRACTION4A419 - 483

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