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- PDB-29mo: Crystal structure of human CLK3 in complex with AZ176 -

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Basic information

Entry
Database: PDB / ID: 29mo
TitleCrystal structure of human CLK3 in complex with AZ176
ComponentsDual specificity protein kinase CLK3
KeywordsTRANSFERASE / CLK3 / Bosutinib / Macrocycle / Kinase / Inhibitor
Function / homology
Function and homology information


dual-specificity kinase / intermediate filament cytoskeleton / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / protein tyrosine kinase activity / protein phosphorylation / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity ...dual-specificity kinase / intermediate filament cytoskeleton / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / protein tyrosine kinase activity / protein phosphorylation / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / RNA binding / nucleoplasm / ATP binding / membrane / identical protein 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
: / IODIDE ION / Dual specificity protein kinase CLK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZerva, A. / Raig, N. / Hanke, T. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC)
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of human CLK3 in complex with AZ176
Authors: Zerva, A. / Raig, N. / Hanke, T. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC)
History
DepositionMar 23, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: 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 CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,70310
Polymers42,3181
Non-polymers1,3849
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint6 kcal/mol
Surface area16360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.777, 45.425, 83.839
Angle α, β, γ (deg.)90.00, 115.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-649-

HOH

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Components

#1: Protein Dual specificity protein kinase CLK3 / CDC-like kinase 3


Mass: 42318.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK3 / Production host: Escherichia coli (E. coli) / References: UniProt: P49761, dual-specificity kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-A1J3A / 3^{3}-methoxy-1^{7}-(2-(2-(4-methylpiperazin-1-yl)ethoxy)ethoxy)-4,7,10-trioxa-2-aza-1(4,6)-quinolina-3(1,2)-benzenacyclodecaphane-1^{3}-carbonitrile


Mass: 563.645 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H37N5O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 3350 0,2M NaI 10% Ethylene Glycol 0.1M bis-tris propane 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 11, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.1→39.28 Å / Num. obs: 22158 / % possible obs: 100 % / Redundancy: 5.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.059 / Rrim(I) all: 0.141 / Χ2: 0.96 / Net I/σ(I): 8.4
Reflection shellResolution: 2.1→2.16 Å / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.796 / Num. measured all: 10157 / Num. unique obs: 1805 / CC1/2: 0.76 / Rpim(I) all: 0.37 / Rrim(I) all: 0.88 / Χ2: 0.98 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→39.25 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.022 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24635 1081 4.9 %RANDOM
Rwork0.20124 ---
obs0.20342 21070 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.291 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0 Å21.38 Å2
2---2.08 Å20 Å2
3---0.71 Å2
Refinement stepCycle: 1 / Resolution: 2.1→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2800 0 58 104 2962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0122928
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162694
X-RAY DIFFRACTIONr_angle_refined_deg1.1471.8393953
X-RAY DIFFRACTIONr_angle_other_deg0.411.7826187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7995343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.918519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.45910479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0520.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023477
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_it1.9353.5631378
X-RAY DIFFRACTIONr_mcbond_other1.923.5641378
X-RAY DIFFRACTIONr_mcangle_it3.026.3951719
X-RAY DIFFRACTIONr_mcangle_other3.0246.3981720
X-RAY DIFFRACTIONr_scbond_it2.3093.7831550
X-RAY DIFFRACTIONr_scbond_other2.3083.7831551
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6826.8392235
X-RAY DIFFRACTIONr_long_range_B_refined5.21634.583275
X-RAY DIFFRACTIONr_long_range_B_other5.21534.583276
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 95 -
Rwork0.272 1538 -
obs--99.94 %

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