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- PDB-4bi2: Scaffold Focused Virtual Screening: Prospective Application to th... -

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Basic information

Entry
Database: PDB / ID: 4bi2
TitleScaffold Focused Virtual Screening: Prospective Application to the Discovery of TTK Inhibitor
ComponentsDUAL SPECIFICITY PROTEIN KINASE TTK
KeywordsTRANSFERASE / MITOSIS
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-7PE / thieno[2,3-c][2,7]naphthyridine / Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsLangdon, S.R. / Westwood, I.M. / van Montfort, R.L.M. / Brown, N. / Blagg, J.
CitationJournal: J.Chem.Inf.Model / Year: 2013
Title: Scaffold-Focused Virtual Screening: Prospective Application to the Discovery of Ttk Inhibitors.
Authors: Langdon, S.R. / Westwood, I.M. / Van Montfort, R.L.M. / Brown, N. / Blagg, J.
History
DepositionApr 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: DUAL SPECIFICITY PROTEIN KINASE TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7365
Polymers36,1151
Non-polymers6214
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.690, 111.600, 112.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / MONOPOLAR SPINDLE KINASE 1


Mass: 36115.258 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 519-808
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): AI / References: UniProt: P33981, dual-specificity kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT / Polyethylene glycol


Mass: 310.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7
#4: Chemical ChemComp-ZO8 / thieno[2,3-c][2,7]naphthyridine


Mass: 186.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H6N2S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE INCLUDING HEXAHISTIDINE TAG IS AS DESCRIBED IN NAT. CHEM. BIOL. 2010, 6, 259-368.

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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: 3.13 Å3/Da / Density % sol: 59.97 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30-45% (V/V) PEG300, SITTING DROP VAPOUR DIFFUSION, 291K, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.11→56.08 Å / Num. obs: 8291 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 4.3 % / Biso Wilson estimate: 108.28 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.5
Reflection shellResolution: 3.11→3.28 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZMC

2zmc


Resolution: 3.11→56.08 Å / Cor.coef. Fo:Fc: 0.9033 / Cor.coef. Fo:Fc free: 0.8652 / SU R Cruickshank DPI: 1.575 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.717 / SU Rfree Blow DPI: 0.339 / SU Rfree Cruickshank DPI: 0.344
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.226 384 4.63 %RANDOM
Rwork0.1937 ---
obs0.1951 8291 99.98 %-
Displacement parametersBiso mean: 86.28 Å2
Baniso -1Baniso -2Baniso -3
1-26.1559 Å20 Å20 Å2
2--6.1735 Å20 Å2
3----32.3294 Å2
Refinement stepCycle: LAST / Resolution: 3.11→56.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 37 3 2000
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012041HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.22771HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d677SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes51HARMONIC2
X-RAY DIFFRACTIONt_gen_planes308HARMONIC5
X-RAY DIFFRACTIONt_it2041HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.51
X-RAY DIFFRACTIONt_other_torsion21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion276SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2375SEMIHARMONIC4
LS refinement shellResolution: 3.11→3.48 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2244 106 4.56 %
Rwork0.2096 2221 -
all0.2103 2327 -
obs--99.98 %
Refinement TLS params.Method: refined / Origin x: 4.9296 Å / Origin y: 32.2326 Å / Origin z: 16.6268 Å
111213212223313233
T-0.1425 Å2-0.0289 Å20.0005 Å2--0.1932 Å20.1026 Å2---0.0492 Å2
L4.9942 °2-1.5026 °2-0.8414 °2-1.5926 °2-0.3436 °2--1.4667 °2
S0.0519 Å °0.4209 Å °0.248 Å °-0.103 Å °-0.0828 Å °-0.106 Å °0.0709 Å °0.0289 Å °0.0309 Å °
Refinement TLS groupSelection details: CHAIN A

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