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- PDB-7clh: Crystal structure of TTK kinase domain in complex with compound 19 -

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Basic information

Entry
Database: PDB / ID: 7clh
TitleCrystal structure of TTK kinase domain in complex with compound 19
ComponentsDual specificity protein kinase TTK
KeywordsTRANSFERASE / Kinase MPS1 TTK Structure-guided drug design
Function / homology
Function and homology information


protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / repair of mitotic kinetochore microtubule attachment defect / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / protein serine/threonine/tyrosine kinase activity ...protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / repair of mitotic kinetochore microtubule attachment defect / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization / chromosome segregation / kinetochore / spindle / protein tyrosine kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / ATP binding / identical protein binding / membrane / nucleus / cytoplasm
Similarity search - Function
Protein kinase Mps1 family / Tetratricopeptide-like helical domain superfamily / 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-G5C / Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKim, H.L. / Cho, H.Y. / Park, Y.W. / Lee, Y.H. / Son, J.B. / Ko, E.H. / Choi, H.G. / Kim, N.D.
CitationJournal: J.Med.Chem. / Year: 2021
Title: X-ray Crystal Structure-Guided Design and Optimization of 7 H -Pyrrolo[2,3- d ]pyrimidine-5-carbonitrile Scaffold as a Potent and Orally Active Monopolar Spindle 1 Inhibitor.
Authors: Lee, Y. / Kim, H. / Kim, H. / Cho, H.Y. / Jee, J.G. / Seo, K.A. / Son, J.B. / Ko, E. / Choi, H.G. / Kim, N.D. / Kim, I.
History
DepositionJul 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein kinase TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3992
Polymers33,0211
Non-polymers3771
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12670 Å2
Unit cell
Length a, b, c (Å)70.801, 109.907, 113.218
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Dual specificity protein kinase TTK / Phosphotyrosine picked threonine-protein kinase / PYT


Mass: 33021.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTK, MPS1, MPS1L1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P33981, dual-specificity kinase
#2: Chemical ChemComp-G5C / 2-[[2-methoxy-4-(2-oxidanylidenepyrrolidin-1-yl)phenyl]amino]-4-(methylamino)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile


Mass: 377.400 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C19H19N7O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.64 Å3/Da / Density % sol: 66.17 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 7-9% PEG 10000, 0.08-0.14 M magnesium acetate, 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 10056 / % possible obs: 99.54 % / Redundancy: 7.4 % / Biso Wilson estimate: 80.19 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.083 / Net I/σ(I): 20.286
Reflection shellResolution: 2.9→2.95 Å / Rmerge(I) obs: 0.805 / Num. unique obs: 502 / CC1/2: 0.856

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B4W

6b4w


Resolution: 2.9→41.02 Å / SU ML: 0.4067 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.4204 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2721 1008 10.04 %
Rwork0.2035 9036 -
obs0.2104 10044 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.36 Å2
Refinement stepCycle: LAST / Resolution: 2.9→41.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2112 0 28 2 2142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00882189
X-RAY DIFFRACTIONf_angle_d1.06792965
X-RAY DIFFRACTIONf_chiral_restr0.0607322
X-RAY DIFFRACTIONf_plane_restr0.0064372
X-RAY DIFFRACTIONf_dihedral_angle_d7.97231325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.060.3751450.26511251X-RAY DIFFRACTION99.57
3.06-3.250.31541360.24561286X-RAY DIFFRACTION99.86
3.25-3.50.28971440.24091266X-RAY DIFFRACTION99.86
3.5-3.850.28871420.20671281X-RAY DIFFRACTION99.93
3.85-4.410.29031450.18311298X-RAY DIFFRACTION99.86
4.41-5.550.25391440.18751300X-RAY DIFFRACTION99.72
5.55-41.020.241520.1981354X-RAY DIFFRACTION98.37

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