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- PDB-6tn9: X-RAY STRUCTURE OF MPS1 IN COMPLEX WITH COMPOUND 16 -

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Basic information

Entry
Database: PDB / ID: 6tn9
TitleX-RAY STRUCTURE OF MPS1 IN COMPLEX WITH COMPOUND 16
ComponentsDual specificity protein kinase TTK
KeywordsCELL CYCLE / Kinase / Mps1
Function / homology
Function and homology information


protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / 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 ...protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / 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 / spindle / kinetochore / protein tyrosine kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / ATP binding / membrane / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Protein kinase Mps1 family / Tetratricopeptide-like helical domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 Mps1 family / Tetratricopeptide-like helical domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-NN5 / Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMarquardt, T. / Holton, S.J. / Schulze, V.K. / Klar, U. / Kosemund, D. / Siemeister, G. / Bader, B. / Prechtl, S. / Briem, H. / Schirok, H. ...Marquardt, T. / Holton, S.J. / Schulze, V.K. / Klar, U. / Kosemund, D. / Siemeister, G. / Bader, B. / Prechtl, S. / Briem, H. / Schirok, H. / Bohlmann, R. / Nguyen, D. / Fernandez-Montalvan, A. / Boemer, U. / Eberspaecher, U. / Brands, M. / Nussbaum, F. / Koppitz, M.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Treating Cancer by Spindle Assembly Checkpoint Abrogation: Discovery of Two Clinical Candidates, BAY 1161909 and BAY 1217389, Targeting MPS1 Kinase.
Authors: Schulze, V.K. / Klar, U. / Kosemund, D. / Wengner, A.M. / Siemeister, G. / Stockigt, D. / Neuhaus, R. / Lienau, P. / Bader, B. / Prechtl, S. / Holton, S.J. / Briem, H. / Marquardt, T. / ...Authors: Schulze, V.K. / Klar, U. / Kosemund, D. / Wengner, A.M. / Siemeister, G. / Stockigt, D. / Neuhaus, R. / Lienau, P. / Bader, B. / Prechtl, S. / Holton, S.J. / Briem, H. / Marquardt, T. / Schirok, H. / Jautelat, R. / Bohlmann, R. / Nguyen, D. / Fernandez-Montalvan, A.E. / Bomer, U. / Eberspaecher, U. / Bruning, M. / Dohr, O. / Raschke, M. / Kreft, B. / Mumberg, D. / Ziegelbauer, K. / Brands, M. / von Nussbaum, F. / Koppitz, M.
History
DepositionDec 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: 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

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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)34,2142
Polymers33,7711
Non-polymers4431
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.351, 112.691, 70.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 33770.758 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTK, MPS1, MPS1L1 / Plasmid: PD-ECO3-MPS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P33981, dual-specificity kinase
#2: Chemical ChemComp-NN5 / [4-[[6-(3,5-dimethyl-4-oxidanyl-phenyl)-[1,2,4]triazolo[1,5-a]pyridin-2-yl]amino]phenyl]-morpholin-4-yl-methanone


Mass: 443.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H25N5O3 / Feature type: SUBJECT OF INVESTIGATION
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: 3.22 Å3/Da / Density % sol: 61.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 25% GLYCEROL, 1.2 M AS, 0.1 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.6→78.57 Å / Num. obs: 10410 / % possible obs: 75.9 % / Observed criterion σ(I): 3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 29
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 46 / % possible all: 17.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN HOUSE

Resolution: 2.6→78.48 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU B: 34.522 / SU ML: 0.294 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.795 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2647 500 4.8 %RANDOM
Rwork0.2176 ---
obs0.2199 9893 75.7 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 191.46 Å2 / Biso mean: 105.192 Å2 / Biso min: 58.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0 Å2-0 Å2
2--4.47 Å20 Å2
3----4.01 Å2
Refinement stepCycle: final / Resolution: 2.6→78.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2097 0 33 0 2130
Biso mean--124.37 --
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192186
X-RAY DIFFRACTIONr_bond_other_d0.0020.022116
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9852957
X-RAY DIFFRACTIONr_angle_other_deg1.0173.0014865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0955258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.57625.46497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.61915407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.712156
X-RAY DIFFRACTIONr_chiral_restr0.1010.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212412
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02465
LS refinement shellResolution: 2.604→2.671 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 8 -
Rwork0.372 140 -
all-148 -
obs--15.13 %
Refinement TLS params.Method: refined / Origin x: 36.312 Å / Origin y: 37.275 Å / Origin z: 31.023 Å
111213212223313233
T0.2003 Å2-0.1446 Å20.0144 Å2-0.206 Å20.0301 Å2--0.1228 Å2
L3.4504 °2-0.6471 °23.4054 °2-0.6753 °2-1.0008 °2--5.9746 °2
S-0.3489 Å °0.3929 Å °0.4337 Å °0.0565 Å °-0.0565 Å °-0.2307 Å °-0.883 Å °0.7929 Å °0.4054 Å °

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