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- PDB-3wyy: CRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH ... -

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Basic information

Entry
Database: PDB / ID: 3wyy
TitleCRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH (E)-3-(4-((6-(((3s,5s,7s)-adamantan-1-yl)amino)-4-amino-5-cyanopyridin-2-yl)amino)-2-(cyanomethoxy)phenyl)-N-(2-methoxyethyl)acrylamide
ComponentsDual specificity protein kinase TTK
KeywordsTRANSFERASE / KINASE / SERINE/THREONINE-PROTEIN KINASE / INHIBITOR COMPLEX / ATP Binding
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 / 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-O17 / Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.05 Å
AuthorsKusakabe, K. / Ide, N. / Daigo, Y. / Itoh, T. / Yamamoto, T. / Kojima, E. / Mitsuoka, Y. / Tadano, G. / Tagashira, S. / Higashino, K. ...Kusakabe, K. / Ide, N. / Daigo, Y. / Itoh, T. / Yamamoto, T. / Kojima, E. / Mitsuoka, Y. / Tadano, G. / Tagashira, S. / Higashino, K. / Okano, Y. / Sato, Y. / Inoue, M. / Iguchi, M. / Kanazawa, T. / Ishioka, Y. / Dohi, K. / Kido, Y. / Sakamoto, S. / Ando, S. / Maeda, M. / Higaki, M. / Yoshizawa, H. / Murai, H. / Nakamura, Y.
CitationJournal: Bioorg.Med.Chem. / Year: 2015
Title: A unique hinge binder of extremely selective aminopyridine-based Mps1 (TTK) kinase inhibitors with cellular activity.
Authors: Kusakabe, K. / Ide, N. / Daigo, Y. / Itoh, T. / Yamamoto, T. / Kojima, E. / Mitsuoka, Y. / Tadano, G. / Tagashira, S. / Higashino, K. / Okano, Y. / Sato, Y. / Inoue, M. / Iguchi, M. / ...Authors: Kusakabe, K. / Ide, N. / Daigo, Y. / Itoh, T. / Yamamoto, T. / Kojima, E. / Mitsuoka, Y. / Tadano, G. / Tagashira, S. / Higashino, K. / Okano, Y. / Sato, Y. / Inoue, M. / Iguchi, M. / Kanazawa, T. / Ishioka, Y. / Dohi, K. / Kido, Y. / Sakamoto, S. / Ando, S. / Maeda, M. / Higaki, M. / Yoshizawa, H. / Murai, H. / Nakamura, Y.
History
DepositionSep 10, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)37,4002
Polymers36,8581
Non-polymers5421
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Dual specificity protein kinase TTK
hetero molecules

A: Dual specificity protein kinase TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8004
Polymers73,7172
Non-polymers1,0832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area1640 Å2
ΔGint-14 kcal/mol
Surface area22850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.587, 106.403, 114.318
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: Mps1 (TTK) Kinase, UNP residues 516-820
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-O17 / (2E)-3-[4-({4-amino-5-cyano-6-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]dec-1-ylamino]pyridin-2-yl}amino)-2-(cyanomethoxy)phenyl]-N-(2-methoxyethyl)prop-2-enamide


Mass: 541.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H35N7O3

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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: 2.91 Å3/Da / Density % sol: 57.76 % / Mosaicity: 1.31 ° / Mosaicity esd: 0.043 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.35M sodium malonate, 7%(w/v) PEG3350, 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: Sep 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 7627 / % possible obs: 90 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.102 / Χ2: 1.573 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allRpim(I) allRrim(I) allΧ2% possible all
3.05-3.13.10.5683680.3470.6710.92393.9
3.1-3.163.10.4483940.2810.5331.07193.6
3.16-3.223.30.4613810.2790.5431.00793.4
3.22-3.293.20.3774010.2320.4461.00792.8
3.29-3.363.20.3393790.2070.41.18790.9
3.36-3.433.20.3043920.1840.3581.09793.1
3.43-3.523.20.2473690.1520.2921.21892
3.52-3.622.90.2373730.1580.2871.36989.4
3.62-3.723.50.1533980.090.1781.91291.9
3.72-3.843.20.1443670.0890.1711.43389.3
3.84-3.983.20.1263790.0780.151.63190.5
3.98-4.143.40.1163850.070.1371.50991.7
4.14-4.333.50.1083830.0640.1261.74590.5
4.33-4.563.70.0873930.0510.1021.98591.2
4.56-4.843.70.0893800.0510.1032.07389.2
4.84-5.213.60.083720.0460.0931.77788.4
5.21-5.743.60.0843890.0480.0971.80589.2
5.74-6.573.50.0883790.0520.1021.81287.5
6.57-8.273.70.0483700.0270.0551.82284.7
8.27-503.40.043750.0240.0472.52978.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation32.15 Å3 Å
Translation32.15 Å3 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→20 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.878 / WRfactor Rfree: 0.2475 / WRfactor Rwork: 0.1944 / FOM work R set: 0.7789 / SU B: 21.827 / SU ML: 0.389 / SU Rfree: 0.4973 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.497 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2806 756 9.9 %RANDOM
Rwork0.2228 ---
obs0.2286 6871 89.62 %-
all-6871 --
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: 122.94 Å2 / Biso mean: 67.148 Å2 / Biso min: 35.66 Å2
Baniso -1Baniso -2Baniso -3
1--4.17 Å2-0 Å20 Å2
2--5.24 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 3.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1971 0 40 0 2011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192056
X-RAY DIFFRACTIONr_angle_refined_deg0.9851.9852796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5865254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.3325.23884
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05915323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.835155
X-RAY DIFFRACTIONr_chiral_restr0.0590.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211542
LS refinement shellResolution: 3.051→3.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 67 -
Rwork0.31 468 -
all-535 -
obs--90.99 %

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