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- PDB-5kz7: Mark2 complex with 7-[(1S)-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-... -

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Basic information

Entry
Database: PDB / ID: 5kz7
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


establishment or maintenance of cell polarity regulating cell shape / microtubule bundle / regulation of microtubule binding / mitochondrion localization / autophagy of mitochondrion / tau-protein kinase / establishment or maintenance of epithelial cell apical/basal polarity / regulation of axonogenesis / establishment of cell polarity / tau-protein kinase activity ...establishment or maintenance of cell polarity regulating cell shape / microtubule bundle / regulation of microtubule binding / mitochondrion localization / autophagy of mitochondrion / tau-protein kinase / establishment or maintenance of epithelial cell apical/basal polarity / regulation of axonogenesis / establishment of cell polarity / tau-protein kinase activity / axon development / activation of protein kinase activity / protein kinase activator activity / regulation of cytoskeleton organization / lateral plasma membrane / regulation of microtubule cytoskeleton organization / actin filament / peptidyl-threonine phosphorylation / neuron migration / tau protein binding / Wnt signaling pathway / microtubule cytoskeleton organization / positive regulation of neuron projection development / peptidyl-serine phosphorylation / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / cadherin binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / lipid binding / dendrite / 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-6Z2 / Serine/threonine-protein kinase MARK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 3.2 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 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)80,8674
Polymers80,1122
Non-polymers7552
Water0
1
A: Serine/threonine-protein kinase MARK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4342
Polymers40,0561
Non-polymers3771
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)40,4342
Polymers40,0561
Non-polymers3771
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.350, 119.350, 98.738
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-6Z2 / 7-[(1~{S})-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-2-(pyridin-3-ylamino)pyrrolo[2,3-d]pyrimidin-6-one


Mass: 377.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H20FN5O

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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: 2.53 Å3/Da / Density % sol: 51.46 % / Mosaicity: 0.809 °
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 / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. obs: 12561 / % possible obs: 69.6 % / Redundancy: 1.4 % / Biso Wilson estimate: 94.78 Å2 / Rmerge(I) obs: 0.131 / Χ2: 1.617 / Net I/av σ(I): 5.235 / Net I/σ(I): 5.6 / Num. measured all: 11068
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.2-3.521.40.42173.3
3.52-3.661.40.317170.6
3.66-3.831.40.26171
3.83-4.031.40.202172.9
4.03-4.281.40.123171.6
4.28-4.61.40.101171.1
4.6-5.061.40.117171.3
5.06-5.781.40.126171
5.78-7.221.50.121167.5
7.22-201.60.06156.1

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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
Starting model: 5EAK

5eak


Resolution: 3.2→19.53 Å / Cor.coef. Fo:Fc: 0.8876 / Cor.coef. Fo:Fc free: 0.8031 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.564
RfactorNum. reflection% reflectionSelection details
Rfree0.2934 635 5.06 %RANDOM
Rwork0.222 ---
obs0.2255 12561 94.88 %-
Displacement parametersBiso max: 144.25 Å2 / Biso mean: 72.41 Å2 / Biso min: 19.35 Å2
Baniso -1Baniso -2Baniso -3
1--6.4635 Å20 Å20 Å2
2---6.4635 Å20 Å2
3---12.9269 Å2
Refine analyzeLuzzati coordinate error obs: 0.615 Å
Refinement stepCycle: final / Resolution: 3.2→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4743 0 56 0 4799
Biso mean--58.06 --
Num. residues----592
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1728SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes113HARMONIC8
X-RAY DIFFRACTIONt_gen_planes692HARMONIC8
X-RAY DIFFRACTIONt_it4896HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion611SEMIHARMONIC5
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_contact5584SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4896HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6607HARMONIC21.21
X-RAY DIFFRACTIONt_omega_torsion1.78
X-RAY DIFFRACTIONt_other_torsion21.83
LS refinement shellResolution: 3.2→3.5 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3652 156 5.04 %
Rwork0.2452 2939 -
all0.2513 3095 -
obs--94.88 %

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