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- PDB-2b1p: inhibitor complex of JNK3 -

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Basic information

Entry
Database: PDB / ID: 2b1p
Titleinhibitor complex of JNK3
ComponentsMitogen-activated protein kinase 10
KeywordsTRANSFERASE / enzyme-inhibitor complex / kinase inhibitor
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-AIZ / BETA-MERCAPTOETHANOL / Mitogen-activated protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSwahn, B.M. / Huerta, F. / Kallin, E. / Malmstrom, J. / Weigelt, T. / Viklund, J. / Womack, P. / Xue, Y. / Ohberg, L.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2005
Title: Design and synthesis of 6-anilinoindazoles as selective inhibitors of c-Jun N-terminal kinase-3
Authors: Swahn, B.M. / Huerta, F. / Kallin, E. / Malmstrom, J. / Weigelt, T. / Viklund, J. / Womack, P. / Xue, Y. / Ohberg, L.
History
DepositionSep 16, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,7324
Polymers41,0661
Non-polymers6663
Water3,387188
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.336, 71.935, 107.306
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 / c-Jun N-terminal kinase 3 / Stress-activated protein kinase JNK3 / MAP kinase p49 3F12


Mass: 41065.555 Da / Num. of mol.: 1 / Fragment: residues 46-400
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P53779, EC: 2.7.1.37
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AIZ / 3-{6-[(2-CHLOROPHENYL)AMINO]-1H-INDAZOL-3-YL}-5-{[4-(DIMETHYLAMINO)BUTANOYL]AMINO}BENZOIC ACID


Mass: 491.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H26ClN5O3
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG400, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9756 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 1.9→36.7 Å / Num. all: 31447 / Num. obs: 31350 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→2 Å / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→36.7 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.188 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1102 3.5 %RANDOM
Rwork0.22 ---
all0.222 31401 --
obs0.22 31350 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.81 Å2
Baniso -1Baniso -2Baniso -3
1-4.66 Å20 Å20 Å2
2---2.38 Å20 Å2
3----2.28 Å2
Refine analyzeLuzzati coordinate error obs: 0.269 Å
Refinement stepCycle: LAST / Resolution: 1.9→36.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2687 0 44 188 2919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222792
X-RAY DIFFRACTIONr_bond_other_d0.0010.022523
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.9863776
X-RAY DIFFRACTIONr_angle_other_deg0.80135890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3915327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44224.297128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.36115502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6151516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023020
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02531
X-RAY DIFFRACTIONr_nbd_refined0.2070.2593
X-RAY DIFFRACTIONr_nbd_other0.1840.22510
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21353
X-RAY DIFFRACTIONr_nbtor_other0.0850.21626
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2155
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2940.28
X-RAY DIFFRACTIONr_mcbond_it0.9531.51710
X-RAY DIFFRACTIONr_mcbond_other0.1641.5659
X-RAY DIFFRACTIONr_mcangle_it1.522692
X-RAY DIFFRACTIONr_scbond_it2.03631226
X-RAY DIFFRACTIONr_scangle_it3.0174.51084
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 90 -
Rwork0.328 2158 -
all-2248 -
obs--97.48 %

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