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- PDB-3pze: JNK1 in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 3pze
TitleJNK1 in complex with inhibitor
ComponentsMitogen-activated protein kinase 8
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase JNK1 / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of cell killing / JUN phosphorylation / regulation of DNA replication origin binding / Interleukin-38 signaling / Activation of BMF and translocation to mitochondria / basal dendrite / Activation of BIM and translocation to mitochondria / JUN kinase activity / WNT5:FZD7-mediated leishmania damping / protein serine/threonine kinase binding ...positive regulation of cell killing / JUN phosphorylation / regulation of DNA replication origin binding / Interleukin-38 signaling / Activation of BMF and translocation to mitochondria / basal dendrite / Activation of BIM and translocation to mitochondria / JUN kinase activity / WNT5:FZD7-mediated leishmania damping / protein serine/threonine kinase binding / positive regulation of cyclase activity / histone deacetylase regulator activity / positive regulation of NLRP3 inflammasome complex assembly / DSCAM interactions / NRAGE signals death through JNK / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / regulation of macroautophagy / mitogen-activated protein kinase / stress-activated MAPK cascade / response to mechanical stimulus / response to UV / JNK cascade / cellular response to cadmium ion / cellular response to amino acid starvation / positive regulation of protein metabolic process / NRIF signals cell death from the nucleus / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / negative regulation of protein binding / FCERI mediated MAPK activation / peptidyl-threonine phosphorylation / regulation of circadian rhythm / cellular response to reactive oxygen species / cellular response to mechanical stimulus / histone deacetylase binding / rhythmic process / regulation of protein localization / cellular senescence / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to oxidative stress / protein phosphatase binding / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / cellular response to lipopolysaccharide / response to oxidative stress / positive regulation of apoptotic process / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / synapse / positive regulation of gene expression / negative regulation of apoptotic process / enzyme binding / nucleoplasm / ATP binding / nucleus / 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-CFK / Mitogen-activated protein kinase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsXue, Y.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Discovery of Checkpoint Kinase Inhibitor (S)-5-(3-Fluorophenyl)-N-(piperidin-3-yl)-3-ureidothiophene-2-carboxamide (AZD7762) by Structure-Based Design and Optimization of Thiophenecarboxamide Ureas.
Authors: Oza, V. / Ashwell, S. / Almeida, L. / Brassil, P. / Breed, J. / Deng, C. / Gero, T. / Grondine, M. / Horn, C. / Ioannidis, S. / Liu, D. / Lyne, P. / Newcombe, N. / Pass, M. / Read, J. / ...Authors: Oza, V. / Ashwell, S. / Almeida, L. / Brassil, P. / Breed, J. / Deng, C. / Gero, T. / Grondine, M. / Horn, C. / Ioannidis, S. / Liu, D. / Lyne, P. / Newcombe, N. / Pass, M. / Read, J. / Ready, S. / Rowsell, S. / Su, M. / Toader, D. / Vasbinder, M. / Yu, D. / Yu, Y. / Xue, Y. / Zabludoff, S. / Janetka, J.
History
DepositionDec 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Database references
Revision 1.2Jun 27, 2012Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Feb 21, 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 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9936
Polymers41,3481
Non-polymers6465
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.586, 71.378, 106.731
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 8 / MAP kinase 8 / MAPK 8 / JNK-46 / Stress-activated protein kinase 1 / Stress-activated protein ...MAP kinase 8 / MAPK 8 / JNK-46 / Stress-activated protein kinase 1 / Stress-activated protein kinase JNK1 / c-Jun N-terminal kinase 1


Mass: 41347.824 Da / Num. of mol.: 1 / Fragment: UNP residues 7-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK8, JNK1, PRKM8, SAPK1 / Production host: Escherichia coli (E. coli)
References: UniProt: P45983, mitogen-activated protein kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CFK / 3-(carbamoylamino)-5-phenylthiophene-2-carboxamide


Mass: 261.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11N3O2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7
Details: 15% PEG2000 MME, 100 mM HEPES, 10 mM DTT, pH 7, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0159
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 15, 2000
RadiationMonochromator: Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0159 Å / Relative weight: 1
ReflectionResolution: 2→31.8 Å / Num. all: 25419 / Num. obs: 25419 / % possible obs: 96.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 25.3 Å2
Reflection shellResolution: 2→2.11 Å / % possible all: 94.7

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
BUSTER2.9.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→23.33 Å / Cor.coef. Fo:Fc: 0.9293 / Cor.coef. Fo:Fc free: 0.9143 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2396 1041 4.11 %RANDOM
Rwork0.2045 ---
obs0.206 25353 96.49 %-
all-25419 --
Displacement parametersBiso max: 132.32 Å2 / Biso mean: 37.2244 Å2 / Biso min: 15.02 Å2
Baniso -1Baniso -2Baniso -3
1--9.4845 Å20 Å20 Å2
2--3.2042 Å20 Å2
3---6.2803 Å2
Refine analyzeLuzzati coordinate error obs: 0.232 Å
Refinement stepCycle: LAST / Resolution: 2→23.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2816 0 38 177 3031
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d10292
X-RAY DIFFRACTIONt_trig_c_planes772
X-RAY DIFFRACTIONt_gen_planes4065
X-RAY DIFFRACTIONt_it291420
X-RAY DIFFRACTIONt_chiral_improper_torsion3685
X-RAY DIFFRACTIONt_ideal_dist_contact35264
X-RAY DIFFRACTIONt_bond_d291420.01
X-RAY DIFFRACTIONt_angle_deg394021.12
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion19.15
LS refinement shellResolution: 2→2.08 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2381 103 3.76 %
Rwork0.2271 2635 -
all0.2274 2738 -
obs--96.49 %

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