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- PDB-3w1f: Crystal structure of Human MPS1 catalytic domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3w1f
TitleCrystal structure of Human MPS1 catalytic domain in complex with 5-(5-ethoxy-6-(1-methyl-1H-pyrazol-4-yl)-1H-indazol-3-yl)-2-methylbenzenesulfonamide
ComponentsDual specificity protein kinase TTK
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / KINASE / SERINE/THREONINE-PROTEIN KINASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / kinetochore / spindle / protein tyrosine kinase activity / phosphorylation / 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 / 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-1O5 / Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsKusakabe, K. / Ide, N. / Daigo, Y. / Tachibana, Y. / Itoh, T. / Yamamoto, T. / Hashizume, H. / Hato, Y. / Higashino, K. / Okano, Y. ...Kusakabe, K. / Ide, N. / Daigo, Y. / Tachibana, Y. / Itoh, T. / Yamamoto, T. / Hashizume, H. / Hato, Y. / Higashino, K. / Okano, Y. / Sato, Y. / Inoue, M. / Iguchi, M. / Kanazawa, T. / Ishioka, Y. / Dohi, K. / Kido, Y. / Sakamoto, S. / Yasuo, K. / Maeda, M. / Higaki, M. / Ueda, K. / Yoshizawa, H. / Baba, Y. / Shiota, T. / Murai, H. / Nakamura, Y.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Indazole-based potent and cell-active Mps1 kinase inhibitors: rational design from pan-kinase inhibitor anthrapyrazolone (SP600125)
Authors: Kusakabe, K. / Ide, N. / Daigo, Y. / Tachibana, Y. / Itoh, T. / Yamamoto, T. / Hashizume, H. / Hato, Y. / Higashino, K. / Okano, Y. / Sato, Y. / Inoue, M. / Iguchi, M. / Kanazawa, T. / ...Authors: Kusakabe, K. / Ide, N. / Daigo, Y. / Tachibana, Y. / Itoh, T. / Yamamoto, T. / Hashizume, H. / Hato, Y. / Higashino, K. / Okano, Y. / Sato, Y. / Inoue, M. / Iguchi, M. / Kanazawa, T. / Ishioka, Y. / Dohi, K. / Kido, Y. / Sakamoto, S. / Yasuo, K. / Maeda, M. / Higaki, M. / Ueda, K. / Yoshizawa, H. / Baba, Y. / Shiota, T. / Murai, H. / Nakamura, Y.
History
DepositionNov 14, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dual specificity protein kinase TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2702
Polymers36,8581
Non-polymers4111
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.773, 108.177, 113.062
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: 36858.363 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 516-820
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTK, MPS1, MPS1L1 / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: P33981, dual-specificity kinase
#2: Chemical ChemComp-1O5 / 5-[5-ethoxy-6-(1-methyl-1H-pyrazol-4-yl)-1H-indazol-3-yl]-2-methylbenzenesulfonamide


Mass: 411.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N5O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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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: 2.94 Å3/Da / Density % sol: 58.1 % / Mosaicity: 0.607 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 11.5% w/v PEG 4000, 0.15M Magnesium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 26, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 11732 / % possible obs: 95.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.053 / Χ2: 1.033 / Net I/σ(I): 17
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.7530.45670.629194.3
2.75-2.82.90.3685880.593197.4
2.8-2.8530.3185740.629196
2.85-2.912.90.2945680.695197.3
2.91-2.972.90.2566180.634196.3
2.97-3.043.10.215690.646198.1
3.04-3.123.10.2045740.742195.5
3.12-3.23.20.1435970.673196.3
3.2-3.33.20.1395930.861196.9
3.3-3.43.30.1095790.869196
3.4-3.523.40.0945840.938196.5
3.52-3.663.40.0825950.978198
3.66-3.833.50.0695941.108197.1
3.83-4.033.40.055850.965193.9
4.03-4.293.50.0445781.207194.1
4.29-4.623.50.0385941.454195.3
4.62-5.083.50.0355911.272194.1
5.08-5.813.60.0385931.43195
5.81-7.323.40.0375991.467193.9
7.32-503.30.0215922.273186.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å28.34 Å
Translation3 Å28.34 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.896 / WRfactor Rfree: 0.2687 / WRfactor Rwork: 0.2208 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7729 / SU B: 13.927 / SU ML: 0.281 / SU R Cruickshank DPI: 0.6289 / SU Rfree: 0.3483 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.629 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2774 1136 9.7 %RANDOM
Rwork0.233 ---
obs0.2374 11672 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 107.56 Å2 / Biso mean: 70.1517 Å2 / Biso min: 36.49 Å2
Baniso -1Baniso -2Baniso -3
1--4.1 Å20 Å20 Å2
2--5.54 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 29 7 2064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222104
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9792861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5095256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.89925.32692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.53215352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.147156
X-RAY DIFFRACTIONr_chiral_restr0.080.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211587
X-RAY DIFFRACTIONr_mcbond_it0.7281.51294
X-RAY DIFFRACTIONr_mcangle_it1.35922087
X-RAY DIFFRACTIONr_scbond_it1.4763810
X-RAY DIFFRACTIONr_scangle_it2.5924.5774
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 86 -
Rwork0.346 747 -
all-833 -
obs--95.53 %

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