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- PDB-6ekd: Crystal structure of JNK3 in complex with a pyridinylimidazole in... -

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Basic information

Entry
Database: PDB / ID: 6ekd
TitleCrystal structure of JNK3 in complex with a pyridinylimidazole inhibitor
ComponentsMitogen-activated protein kinase 10
KeywordsTRANSFERASE / Protein Kinase Activity Map Kinase Activity ATP Binding Protein Phosphorylation
Function / homology
Function and homology information


JUN kinase activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / response to light stimulus / mitogen-activated protein kinase / JNK cascade / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / FCERI mediated MAPK activation / regulation of circadian rhythm ...JUN kinase activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / response to light stimulus / mitogen-activated protein kinase / JNK cascade / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / FCERI mediated MAPK activation / regulation of circadian rhythm / cellular senescence / rhythmic process / Oxidative Stress Induced Senescence / protein phosphorylation / protein serine kinase activity / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Mitogen-activated protein (MAP) kinase, JNK / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Mitogen-activated protein (MAP) kinase, JNK / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-B9K / BETA-MERCAPTOETHANOL / Mitogen-activated protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMacedo, J.T. / Stehle, T. / Blaum, B.S.
CitationJournal: ACS Omega / Year: 2018
Title: Structural Optimization of a Pyridinylimidazole Scaffold: Shifting the Selectivity from p38 alpha Mitogen-Activated Protein Kinase to c-Jun N-Terminal Kinase 3.
Authors: Ansideri, F. / Macedo, J.T. / Eitel, M. / El-Gokha, A. / Zinad, D.S. / Scarpellini, C. / Kudolo, M. / Schollmeyer, D. / Boeckler, F.M. / Blaum, B.S. / Laufer, S.A. / Koch, P.
History
DepositionSep 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7834
Polymers42,2611
Non-polymers5223
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-0 kcal/mol
Surface area15730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.510, 124.820, 68.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Mitogen-activated protein kinase 10 / MAPK 10 / MAP kinase p49 3F12 / Stress-activated protein kinase 1b / SAPK1b / Stress-activated ...MAPK 10 / MAP kinase p49 3F12 / Stress-activated protein kinase 1b / SAPK1b / Stress-activated protein kinase JNK3 / c-Jun N-terminal kinase 3


Mass: 42260.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK10, JNK3, JNK3A, PRKM10, SAPK1B / Production host: Escherichia coli (E. coli)
References: UniProt: P53779, mitogen-activated protein kinase
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-B9K / 4-(4-methyl-2-methylsulfanyl-1~{H}-imidazol-5-yl)-~{N}-(4-morpholin-4-ylphenyl)pyridin-2-amine


Mass: 381.495 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N5OS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.07 Å3/Da / Density % sol: 40.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Bis Tris pH 5.5, 200 mM NaCl, 29% PEG 3350, 1 mM AMP-PCP, 0.4 mM Zwittergent 3-14, 10% Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 20913 / % possible obs: 100 % / Redundancy: 25.8 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 26.4
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 2.982

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X21

4x21


Resolution: 2.1→48.48 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 13.325 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.204 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25902 1046 5 %RANDOM
Rwork0.2056 ---
obs0.20817 19867 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.355 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å2-0 Å20 Å2
2---0.1 Å2-0 Å2
3---0.78 Å2
Refinement stepCycle: 1 / Resolution: 2.1→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2539 0 35 104 2678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192653
X-RAY DIFFRACTIONr_bond_other_d0.0020.022438
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9743597
X-RAY DIFFRACTIONr_angle_other_deg0.9835650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0185328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.30124.685111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14515453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6471510
X-RAY DIFFRACTIONr_chiral_restr0.0950.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212908
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02514
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0462.4881306
X-RAY DIFFRACTIONr_mcbond_other1.0462.4881305
X-RAY DIFFRACTIONr_mcangle_it1.7263.7231630
X-RAY DIFFRACTIONr_mcangle_other1.7253.7241631
X-RAY DIFFRACTIONr_scbond_it1.242.6141347
X-RAY DIFFRACTIONr_scbond_other1.2362.6141347
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7643.8691966
X-RAY DIFFRACTIONr_long_range_B_refined4.48530.0092996
X-RAY DIFFRACTIONr_long_range_B_other4.48430.0362997
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 77 -
Rwork0.333 1459 -
obs--99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.44231.33211.54774.05860.39036.27330.17090.0209-0.1317-0.0365-0.28570.30930.0582-0.33210.11470.1480.02650.01740.2215-0.09440.085810.534347.260414.4557
21.16350.8679-0.48345.86830.19661.3972-0.0748-0.0617-0.0211-0.07270.0321-0.1337-0.03010.08370.04270.12320.0211-0.0160.2888-0.07630.11617.042840.00046.6906
31.7464-0.6552-0.44495.2049-0.02933.1204-0.0682-0.58610.11850.3516-0.008-0.1574-0.07860.58920.07610.1235-0.0169-0.02810.374-0.03020.028719.378619.74246.2794
41.78750.4533-0.27296.16920.78140.9824-0.0422-0.1928-0.24810.06650.0402-0.16890.18610.31970.0020.15850.0823-0.00110.35590.03240.037721.85115.66973.2946
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 87
2X-RAY DIFFRACTION2A88 - 162
3X-RAY DIFFRACTION3A163 - 279
4X-RAY DIFFRACTION4A280 - 400

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