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- PDB-5kz8: Mark2 complex with 7-[(1S)-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-... -

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Basic information

Entry
Database: PDB / ID: 5kz8
TitleMark2 complex with 7-[(1S)-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-2-(3-pyridylamino)pyrrolo[2,3-d]pyrimidin-6-one
ComponentsSerine/threonine-protein kinase MARK2
KeywordsTransferase/Transferase Inhibitor / Mark / Serine/threonine-protein kinase / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


microtubule bundle / establishment or maintenance of cell polarity regulating cell shape / regulation of neurofibrillary tangle assembly / establishment or maintenance of epithelial cell apical/basal polarity / tau-protein kinase / autophagy of mitochondrion / mitochondrion localization / tau-protein kinase activity / regulation of axonogenesis / axon development ...microtubule bundle / establishment or maintenance of cell polarity regulating cell shape / regulation of neurofibrillary tangle assembly / establishment or maintenance of epithelial cell apical/basal polarity / tau-protein kinase / autophagy of mitochondrion / mitochondrion localization / tau-protein kinase activity / regulation of axonogenesis / axon development / regulation of cytoskeleton organization / establishment of cell polarity / lateral plasma membrane / protein kinase activator activity / regulation of microtubule cytoskeleton organization / actin filament / positive regulation of neuron projection development / peptidyl-serine phosphorylation / microtubule cytoskeleton organization / tau protein binding / Wnt signaling pathway / neuron migration / protein autophosphorylation / protein phosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / cadherin binding / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / lipid binding / magnesium ion binding / mitochondrion / RNA binding / nucleoplasm / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Serine/threonine-protein kinase, active site ...: / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / 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-6Z5 / Serine/threonine-protein kinase MARK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 3.21 Å
AuthorsSu, H.P. / Munshi, S.K.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: Structure guided design of a series of selective pyrrolopyrimidinone MARK inhibitors.
Authors: Katz, J.D. / Haidle, A. / Childers, K.K. / Zabierek, A.A. / Jewell, J.P. / Hou, Y. / Altman, M.D. / Szewczak, A. / Chen, D. / Harsch, A. / Hayashi, M. / Warren, L. / Hutton, M. / Nuthall, H. ...Authors: Katz, J.D. / Haidle, A. / Childers, K.K. / Zabierek, A.A. / Jewell, J.P. / Hou, Y. / Altman, M.D. / Szewczak, A. / Chen, D. / Harsch, A. / Hayashi, M. / Warren, L. / Hutton, M. / Nuthall, H. / Su, H.P. / Munshi, S. / Stanton, M.G. / Davies, I.W. / Munoz, B. / Northrup, A.
History
DepositionJul 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase MARK2
B: Serine/threonine-protein kinase MARK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8814
Polymers80,1122
Non-polymers7692
Water00
1
A: Serine/threonine-protein kinase MARK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4412
Polymers40,0561
Non-polymers3841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase MARK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4412
Polymers40,0561
Non-polymers3841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.416, 120.416, 99.457
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Serine/threonine-protein kinase MARK2 / ELKL motif kinase 1 / EMK-1 / MAP/microtubule affinity-regulating kinase 2 / PAR1 homolog / PAR1 ...ELKL motif kinase 1 / EMK-1 / MAP/microtubule affinity-regulating kinase 2 / PAR1 homolog / PAR1 homolog b / Par1b


Mass: 40056.090 Da / Num. of mol.: 2 / Fragment: UNP residues 6-331
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MARK2, EMK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7KZI7, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Chemical ChemComp-6Z5 / 5,5-dimethyl-7-[(1~{S})-4-oxidanyl-1~{H}-inden-1-yl]-2-phenylazanyl-pyrrolo[2,3-d]pyrimidin-6-one


Mass: 384.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H20N4O2

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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: 52.66 % / Mosaicity: 0.628 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M BIS-TRIS PH 6.5, 14% PEG3350, 200MM AMM.SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.2→100 Å / Num. obs: 13540 / % possible obs: 99.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 110.7 Å2 / Rmerge(I) obs: 0.153 / Χ2: 1.125 / Net I/av σ(I): 10.058 / Net I/σ(I): 8.1 / Num. measured all: 71083
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.2-3.3150.78913431.357100
3.31-3.455.20.57413331.182100
3.45-3.65.20.4213561.147100
3.6-3.795.30.29113431.164100
3.79-4.035.30.18713431.076100
4.03-4.345.30.13913561.032100
4.34-4.785.40.10913491.064100
4.78-5.475.40.11213611.016100
5.47-6.895.30.11213591.00699.9
6.89-1005.10.04313971.23199.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.21→44.89 Å / Cor.coef. Fo:Fc: 0.9044 / Cor.coef. Fo:Fc free: 0.8219 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.537
RfactorNum. reflection% reflectionSelection details
Rfree0.2903 688 5.11 %RANDOM
Rwork0.2187 ---
obs0.2222 13471 99.87 %-
Displacement parametersBiso max: 164.64 Å2 / Biso mean: 76.49 Å2 / Biso min: 18.98 Å2
Baniso -1Baniso -2Baniso -3
1--2.3665 Å20 Å20 Å2
2---2.3665 Å20 Å2
3---4.7331 Å2
Refine analyzeLuzzati coordinate error obs: 0.672 Å
Refinement stepCycle: final / Resolution: 3.21→44.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4830 0 58 0 4888
Biso mean--59.13 --
Num. residues----602
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1769SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes117HARMONIC8
X-RAY DIFFRACTIONt_gen_planes729HARMONIC8
X-RAY DIFFRACTIONt_it4994HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion621SEMIHARMONIC5
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_contact5778SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4994HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6747HARMONIC21.25
X-RAY DIFFRACTIONt_omega_torsion1.77
X-RAY DIFFRACTIONt_other_torsion21.63
LS refinement shellResolution: 3.21→3.47 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3189 147 5.32 %
Rwork0.2527 2617 -
all0.2562 2764 -
obs--99.87 %

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