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- PDB-6tnd: X-RAY STRUCTURE OF MPS1 IN COMPLEX WITH COMPOUND 79 -

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Basic information

Entry
Database: PDB / ID: 6tnd
TitleX-RAY STRUCTURE OF MPS1 IN COMPLEX WITH COMPOUND 79
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
BAY 1217389 / Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsHolton, S.J. / Schulze, V.K. / Klar, U. / Kosemund, D. / Siemeister, G. / Bader, B. / Prechtl, S. / Briem, H. / Marquardt, T. / Schirok, H. ...Holton, S.J. / Schulze, V.K. / Klar, U. / Kosemund, D. / Siemeister, G. / Bader, B. / Prechtl, S. / Briem, H. / Marquardt, T. / 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)34,3322
Polymers33,7711
Non-polymers5621
Water70339
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 area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.130, 107.800, 112.896
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTK, MPS1, MPS1L1 / Production host: Escherichia coli (E. coli) / References: UniProt: P33981, dual-specificity kinase
#2: Chemical ChemComp-8RH / BAY 1217389


Mass: 561.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H24F5N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.65 Å3/Da / Density % sol: 66.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 10% PEG 3350, 180mM Magnesium formate, 25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.58→40.91 Å / Num. obs: 14027 / % possible obs: 99.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 7.1
Reflection shellResolution: 2.58→2.73 Å / Rmerge(I) obs: 0.484 / Num. unique obs: 1943

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→40.91 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.919 / SU B: 18.923 / SU ML: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.335 / ESU R Free: 0.264
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 702 5 %RANDOM
Rwork0.1865 ---
obs0.1897 13325 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 154.3 Å2 / Biso mean: 60.329 Å2 / Biso min: 30.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0 Å2-0 Å2
2--0.75 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 2.58→40.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 40 39 2158
Biso mean--57.83 54.27 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132183
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172038
X-RAY DIFFRACTIONr_angle_refined_deg2.0141.6652957
X-RAY DIFFRACTIONr_angle_other_deg1.3421.5884737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4445254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.9124.615104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.73315407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.382156
X-RAY DIFFRACTIONr_chiral_restr0.0960.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022349
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02398
LS refinement shellResolution: 2.58→2.646 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.334 51 -
Rwork0.334 958 -
obs--99.61 %
Refinement TLS params.Method: refined / Origin x: -4.624 Å / Origin y: -16.755 Å / Origin z: -36.199 Å
111213212223313233
T0.0163 Å20.0148 Å20.0127 Å2-0.1966 Å20.0676 Å2--0.0797 Å2
L2.7504 °2-0.1511 °2-1.2484 °2-0.1737 °20.2054 °2--1.5948 °2
S0.1441 Å °0.1503 Å °0.3888 Å °-0.0172 Å °0.0704 Å °0.0292 Å °0.0051 Å °-0.0455 Å °-0.2146 Å °

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