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- PDB-3g9n: JNK3 bound to (Z)-1-((6-fluoro-4H-benzo[d][1,3]dioxin-8-yl)methyl... -

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Basic information

Entry
Database: PDB / ID: 3g9n
TitleJNK3 bound to (Z)-1-((6-fluoro-4H-benzo[d][1,3]dioxin-8-yl)methyl)-3-(hydroxyimino)-4-phenylindolin-2-one
ComponentsMitogen-activated protein kinase 10
KeywordsTRANSFERASE / kinase / inhibitor / phosphorylation / ATP-binding / Epilepsy / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase
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 / rhythmic process / cellular senescence / Oxidative Stress Induced Senescence / protein phosphorylation / protein serine kinase activity / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase, JNK / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Mitogen-activated protein (MAP) kinase, JNK / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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-J88 / Mitogen-activated protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsJacobs, M.D.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Structure-based design and parallel synthesis of N-benzyl isatin oximes as JNK3 MAP kinase inhibitors.
Authors: Cao, J. / Gao, H. / Bemis, G. / Salituro, F. / Ledeboer, M. / Harrington, E. / Wilke, S. / Taslimi, P. / Pazhanisamy, S. / Xie, X. / Jacobs, M. / Green, J.
History
DepositionFeb 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)42,5212
Polymers42,1171
Non-polymers4041
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.313, 72.176, 107.489
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 Mitogen-activated protein kinase 10 / Stress-activated protein kinase JNK3 / c-Jun N-terminal kinase 3 / MAP kinase p49 3F12


Mass: 42116.727 Da / Num. of mol.: 1 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JNK3, JNK3A, MAPK10, PRKM10 / Plasmid: pET-15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P53779, mitogen-activated protein kinase
#2: Chemical ChemComp-J88 / (3Z)-1-[(6-fluoro-4H-1,3-benzodioxin-8-yl)methyl]-4-phenyl-1H-indole-2,3-dione 3-oxime


Mass: 404.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H17FN2O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18-20% (v/v) polyethylene glycol monomethyl ether (average Mr = 550), 10% (v/v) ethylene glycol, 20 mM beta-mercaptoethanol, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 2, 1999
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→59.87 Å / Num. obs: 9652 / % possible obs: 82.4 % / Rmerge(I) obs: 0.098 / Χ2: 1.165 / Net I/σ(I): 8.501
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.90.2877530.899175.5
2.9-3.020.2547651.021176.6
3.02-3.150.217911.063178.9
3.15-3.320.177991.141181.8
3.32-3.530.1428401.176184.1
3.53-3.80.18741.053186
3.8-4.180.0848801.072187
4.18-4.790.0798821.333187.1
4.79-6.030.0778891.279185.4
6.03-550.0669071.375181.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
CNXphasing
RefinementResolution: 2.8→55 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.809 / WRfactor Rfree: 0.308 / WRfactor Rwork: 0.224 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.773 / SU B: 21.372 / SU ML: 0.418 / SU R Cruickshank DPI: 0.406 / SU Rfree: 0.542 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.525 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.326 472 4.9 %RANDOM
Rwork0.226 ---
obs0.23 9652 95.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.8 Å2 / Biso mean: 37.763 Å2 / Biso min: 8.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.37 Å20 Å20 Å2
2---3.11 Å20 Å2
3----2.26 Å2
Refinement stepCycle: LAST / Resolution: 2.8→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2804 0 30 7 2841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222907
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.9823938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6085344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.35724.361133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.15215521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3381516
X-RAY DIFFRACTIONr_chiral_restr0.090.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022189
X-RAY DIFFRACTIONr_nbd_refined0.2380.21339
X-RAY DIFFRACTIONr_nbtor_refined0.310.21955
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2107
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.21
X-RAY DIFFRACTIONr_mcbond_it0.4831.51780
X-RAY DIFFRACTIONr_mcangle_it0.85222826
X-RAY DIFFRACTIONr_scbond_it0.90431285
X-RAY DIFFRACTIONr_scangle_it1.4234.51112
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 41 -
Rwork0.35 610 -
all-651 -
obs--89.3 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Origin x: 0 Å / Origin y: 0 Å / Origin z: 0 Å / Refine-ID: X-RAY DIFFRACTION

ID
1
2
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 149
2X-RAY DIFFRACTION1A217 - 225
3X-RAY DIFFRACTION1A372 - 500
4X-RAY DIFFRACTION2A150 - 216
5X-RAY DIFFRACTION2A226 - 371

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