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- PDB-5iha: MELK in complex with NVS-MELK8F -

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Basic information

Entry
Database: PDB / ID: 5iha
TitleMELK in complex with NVS-MELK8F
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 / protein autophosphorylation / cell population proliferation / 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 / protein autophosphorylation / cell population proliferation / non-specific serine/threonine protein kinase / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / lipid binding / calcium ion binding / apoptotic process / 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-6BE / Maternal embryonic leucine zipper kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.96 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)39,3512
Polymers38,9591
Non-polymers3921
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.152, 67.633, 104.651
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-6BE / 1-methyl-4-(4-{4-[3-(2-methylpropoxy)pyridin-4-yl]-1H-pyrazol-1-yl}phenyl)piperazine


Mass: 391.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H29N5O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.6 Å3/Da / Density % sol: 52.62 %
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: Feb 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.955→67.633 Å / Num. all: 29987 / Num. obs: 29987 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 32.6 Å2 / Rpim(I) all: 0.024 / Rrim(I) all: 0.058 / Rsym value: 0.052 / Net I/av σ(I): 9.973 / Net I/σ(I): 18.9 / Num. measured all: 160298
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.96-2.065.40.491.51100
2.06-2.195.40.292.61100
2.19-2.345.60.1844.1199.9
2.34-2.525.30.1295.8199.9
2.52-2.775.40.0858.8199.9
2.77-3.095.50.05612.8199.9
3.09-3.575.10.0416.7199.5
3.57-4.375.30.03219.6199.5
4.37-6.1850.0318.8198.9
6.18-67.6334.80.02818.1198.7

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.20data scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.2data extraction
RefinementResolution: 1.96→24.77 Å / Cor.coef. Fo:Fc: 0.9416 / Cor.coef. Fo:Fc free: 0.9255 / SU R Cruickshank DPI: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.135 / SU Rfree Blow DPI: 0.122 / SU Rfree Cruickshank DPI: 0.12
RfactorNum. reflection% reflectionSelection details
Rfree0.2022 1461 4.92 %RANDOM
Rwork0.1733 ---
obs0.1747 29693 99.66 %-
Displacement parametersBiso max: 131.57 Å2 / Biso mean: 41.52 Å2 / Biso min: 21.53 Å2
Baniso -1Baniso -2Baniso -3
1--16.5378 Å20 Å20 Å2
2--8.4027 Å20 Å2
3---8.1351 Å2
Refine analyzeLuzzati coordinate error obs: 0.222 Å
Refinement stepCycle: final / Resolution: 1.96→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 0 29 203 2718
Biso mean--41.98 48.11 -
Num. residues----303
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d921SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes63HARMONIC2
X-RAY DIFFRACTIONt_gen_planes361HARMONIC5
X-RAY DIFFRACTIONt_it2590HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion323SEMIHARMONIC5
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_contact3073SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2590HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3503HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion16.62
LS refinement shellResolution: 1.96→2.03 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2257 143 5.01 %
Rwork0.1978 2712 -
all0.1993 2855 -
obs--99.66 %
Refinement TLS params.Method: refined / Origin x: -2.9651 Å / Origin y: -2.7537 Å / Origin z: 10.4566 Å
111213212223313233
T-0.0091 Å2-0.0075 Å20.0165 Å2--0.1085 Å2-0.0043 Å2---0.0905 Å2
L0.7782 °2-0.2862 °20.3526 °2-1.437 °2-0.6503 °2--1.3562 °2
S0.0089 Å °0.0145 Å °0.0052 Å °-0.1129 Å °-0.0064 Å °0.0343 Å °0.0214 Å °-0.0553 Å °-0.0025 Å °
Refinement TLS groupSelection details: { A|* }

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