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- PDB-4w4w: JNK2/3 in complex with N-(2-methylpyridin-4-yl)-3-{4-[(phenylcarb... -

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Basic information

Entry
Database: PDB / ID: 4w4w
TitleJNK2/3 in complex with N-(2-methylpyridin-4-yl)-3-{4-[(phenylcarbamoyl)amino]-1H-pyrazol-1-yl}benzamide
Componentsc-Jun N-terminal kinase 3
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / JNK / MAP kinase / isoform selective / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / 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. ...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-3HJ / Mitogen-activated protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsPark, H. / Iqbal, S. / Hernandez, P. / Mora, R. / Zheng, K. / Feng, Y. / LoGrasso, P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103825 United States
Department of Defense (DOD, United States)W81XWH-12-1-0431 United States
CitationJournal: Sci Rep / Year: 2015
Title: Structural Basis and Biological Consequences for JNK2/3 Isoform Selective Aminopyrazoles.
Authors: Park, H. / Iqbal, S. / Hernandez, P. / Mora, R. / Zheng, K. / Feng, Y. / LoGrasso, P.
History
DepositionAug 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_detector / entity_src_gen / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 10, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: 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: c-Jun N-terminal kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6742
Polymers42,2621
Non-polymers4121
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.360, 71.040, 107.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein c-Jun N-terminal kinase 3 / 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 / Mitogen-activated protein kinase 10


Mass: 42261.945 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-3HJ / N-(2-methylpyridin-4-yl)-3-{4-[(phenylcarbamoyl)amino]-1H-pyrazol-1-yl}benzamide


Mass: 412.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H20N6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, ammonium tartrate / PH range: 7.0-7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.127 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.9→24.56 Å / Biso Wilson estimate: 28.32 Å2

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Processing

SoftwareName: BUSTER / Version: 2.11.5 / Classification: refinement
RefinementResolution: 1.9→24.56 Å / Cor.coef. Fo:Fc: 0.9404 / Cor.coef. Fo:Fc free: 0.9314 / SU R Cruickshank DPI: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.155 / SU Rfree Blow DPI: 0.134 / SU Rfree Cruickshank DPI: 0.13
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1616 5 %RANDOM
Rwork0.1917 ---
obs0.1931 32304 99.66 %-
Displacement parametersBiso mean: 43.62 Å2
Baniso -1Baniso -2Baniso -3
1--13.8338 Å20 Å20 Å2
2--7.0389 Å20 Å2
3---6.7949 Å2
Refine analyzeLuzzati coordinate error obs: 0.285 Å
Refinement stepCycle: LAST / Resolution: 1.9→24.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2827 0 31 286 3144
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012925HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.063959HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1030SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes412HARMONIC5
X-RAY DIFFRACTIONt_it2925HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion18.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion370SEMIHARMONIC5
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_contact3614SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.96 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2621 148 5.01 %
Rwork0.2544 2808 -
all0.2548 2956 -
obs--99.66 %
Refinement TLS params.Method: refined / Origin x: 9.4661 Å / Origin y: -19.8553 Å / Origin z: -23.2082 Å
111213212223313233
T0.0197 Å20.0021 Å2-0.0221 Å2--0.0714 Å20.0132 Å2---0.0381 Å2
L0.3485 °20.0412 °20.1952 °2-2.1161 °2-0.6768 °2--1.592 °2
S-0.0046 Å °-0.0194 Å °0.0166 Å °0.1782 Å °-0.0877 Å °-0.2048 Å °-0.077 Å °0.1013 Å °0.0923 Å °
Refinement TLS groupSelection details: { A|* }

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