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- PDB-5ihc: MELK in complex with NVS-MELK12B -

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Basic information

Entry
Database: PDB / ID: 5ihc
TitleMELK in complex with NVS-MELK12B
ComponentsMaternal embryonic leucine zipper kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase UBA domain inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


neural precursor cell proliferation / intrinsic apoptotic signaling pathway in response to oxidative stress / hemopoiesis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / G2/M transition of mitotic cell cycle / cell cortex / cell population proliferation / protein autophosphorylation / non-specific serine/threonine protein kinase ...neural precursor cell proliferation / intrinsic apoptotic signaling pathway in response to oxidative stress / hemopoiesis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / G2/M transition of mitotic cell cycle / cell cortex / cell population proliferation / protein autophosphorylation / non-specific serine/threonine protein kinase / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / lipid binding / apoptotic process / calcium ion binding / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Maternal embryonic leucine zipper kinase, catalytic domain / : / Maternal embryonic leucine zipper kinase, UBA domain / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Maternal embryonic leucine zipper kinase, catalytic domain / : / Maternal embryonic leucine zipper kinase, UBA domain / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / 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
Similarity search - Domain/homology
Chem-6BB / Maternal embryonic leucine zipper kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.14 Å
AuthorsSprague, E.R. / Brazell, T.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Toward the Validation of Maternal Embryonic Leucine Zipper Kinase: Discovery, Optimization of Highly Potent and Selective Inhibitors, and Preliminary Biology Insight.
Authors: Toure, B.B. / Giraldes, J. / Smith, T. / Sprague, E.R. / Wang, Y. / Mathieu, S. / Chen, Z. / Mishina, Y. / Feng, Y. / Yan-Neale, Y. / Shakya, S. / Chen, D. / Meyer, M. / Puleo, D. / Brazell, ...Authors: Toure, B.B. / Giraldes, J. / Smith, T. / Sprague, E.R. / Wang, Y. / Mathieu, S. / Chen, Z. / Mishina, Y. / Feng, Y. / Yan-Neale, Y. / Shakya, S. / Chen, D. / Meyer, M. / Puleo, D. / Brazell, J.T. / Straub, C. / Sage, D. / Wright, K. / Yuan, Y. / Chen, X. / Duca, J. / Kim, S. / Tian, L. / Martin, E. / Hurov, K. / Shao, W.
History
DepositionFeb 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maternal embryonic leucine zipper kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3112
Polymers38,9591
Non-polymers3521
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.370, 67.810, 103.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Maternal embryonic leucine zipper kinase / hMELK / Protein kinase Eg3 / pEg3 kinase / Protein kinase PK38 / hPK38 / Tyrosine-protein kinase MELK


Mass: 38959.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MELK, KIAA0175 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q14680, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-6BB / 4-[1-(2-fluorophenyl)-1H-pyrazol-4-yl]-3-[(piperidin-4-yl)methoxy]pyridine


Mass: 352.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21FN4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100mM Hepes, pH 7.6, 0.2M NaCl, 4.5-16.5% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→67.82 Å / Num. obs: 22899 / % possible obs: 99.4 % / Redundancy: 5.4 % / Biso Wilson estimate: 45.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.021 / Rrim(I) all: 0.05 / Net I/σ(I): 19.6 / Num. measured all: 123757
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.14-2.395.60.376199.8
4.78-67.825.10.026197.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.1.27data scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.2data extraction
RefinementResolution: 2.14→40.36 Å / Cor.coef. Fo:Fc: 0.9483 / Cor.coef. Fo:Fc free: 0.9288 / SU R Cruickshank DPI: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.182 / SU Rfree Blow DPI: 0.153 / SU Rfree Cruickshank DPI: 0.152
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 1131 4.96 %RANDOM
Rwork0.1779 ---
obs0.1794 22782 99.06 %-
Displacement parametersBiso max: 146.37 Å2 / Biso mean: 55.08 Å2 / Biso min: 27.88 Å2
Baniso -1Baniso -2Baniso -3
1--13.706 Å20 Å20 Å2
2--8.6146 Å20 Å2
3---5.0914 Å2
Refine analyzeLuzzati coordinate error obs: 0.264 Å
Refinement stepCycle: final / Resolution: 2.14→40.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 52 106 2656
Biso mean--48.45 56.47 -
Num. residues----305
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d929SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes64HARMONIC2
X-RAY DIFFRACTIONt_gen_planes365HARMONIC5
X-RAY DIFFRACTIONt_it2621HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion324SEMIHARMONIC5
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_contact3058SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2621HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3546HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion18.08
LS refinement shellResolution: 2.14→2.24 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2091 153 5.13 %
Rwork0.1895 2832 -
all0.1906 2985 -
obs--99.06 %
Refinement TLS params.Method: refined / Origin x: -3.1793 Å / Origin y: -2.9762 Å / Origin z: 10.4043 Å
111213212223313233
T-0.0835 Å2-0.0248 Å20.0178 Å2--0.1703 Å2-0.013 Å2---0.152 Å2
L1.5674 °2-0.388 °20.6402 °2-1.9633 °2-0.6012 °2--2.1234 °2
S-0.0321 Å °0.0451 Å °0.0323 Å °-0.1005 Å °-0.0191 Å °0.0671 Å °-0.1061 Å °-0.0765 Å °0.0511 Å °
Refinement TLS groupSelection details: { A|* }

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