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- PDB-4w4x: JNK2/3 in complex with 3-(4-{[(4-fluorophenyl)carbamoyl]amino}-1H... -

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Basic information

Entry
Database: PDB / ID: 4w4x
TitleJNK2/3 in complex with 3-(4-{[(4-fluorophenyl)carbamoyl]amino}-1H-pyrazol-1-yl)-N-(2-methylpyridin-4-yl)benzamide
Componentsc-jun NH2-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-3HN / Mitogen-activated protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.65 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 20, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 10, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 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 NH2-terminal kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6922
Polymers42,2621
Non-polymers4301
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.500, 71.440, 107.640
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 NH2-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 / c-Jun N-terminal kinase 3 / 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-3HN / 3-(4-{[(4-fluorophenyl)carbamoyl]amino}-1H-pyrazol-1-yl)-N-(2-methylpyridin-4-yl)benzamide


Mass: 430.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H19FN6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.65→47.19 Å / Biso Wilson estimate: 59.6 Å2

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Processing

SoftwareName: BUSTER / Version: 2.11.5 / Classification: refinement
RefinementResolution: 2.65→47.19 Å / Cor.coef. Fo:Fc: 0.9328 / Cor.coef. Fo:Fc free: 0.8918 / SU R Cruickshank DPI: 1.748 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.378 / SU Rfree Cruickshank DPI: 0.371
RfactorNum. reflection% reflectionSelection details
Rfree0.2838 610 5.02 %RANDOM
Rwork0.1922 ---
obs0.1968 12151 98.89 %-
Displacement parametersBiso mean: 50.73 Å2
Baniso -1Baniso -2Baniso -3
1--10.6037 Å20 Å20 Å2
2--6.0351 Å20 Å2
3---4.5686 Å2
Refine analyzeLuzzati coordinate error obs: 0.392 Å
Refinement stepCycle: LAST / Resolution: 2.65→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 32 160 2956
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012880HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.223912HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1012SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes405HARMONIC5
X-RAY DIFFRACTIONt_it2880HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion20.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion363SEMIHARMONIC5
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_contact3358SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.9 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2876 143 4.99 %
Rwork0.2212 2720 -
all0.2246 2863 -
obs--98.89 %
Refinement TLS params.Method: refined / Origin x: -9.0442 Å / Origin y: 20.0217 Å / Origin z: -23.1145 Å
111213212223313233
T0.0111 Å2-0.0048 Å20.0049 Å2--0.2122 Å2-0.0291 Å2---0.2063 Å2
L0.3344 °2-0.1149 °2-0.4768 °2-3.1037 °21.0201 °2--3.1914 °2
S0.0222 Å °0.0081 Å °-0.0368 Å °0.0943 Å °-0.16 Å °0.2442 Å °0.1717 Å °-0.1183 Å °0.1378 Å °
Refinement TLS groupSelection details: { A|* }

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