|Entry||Database: PDB / ID: 3pze|
|Title||JNK1 in complex with inhibitor|
|Components||Mitogen-activated protein kinase 8|
|Keywords||TRANSFERASE/TRANSFERASE INHIBITOR / kinase JNK1 / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex|
|Function / homology|
Function and homology information
NRAGE signals death through JNK / Oxidative Stress Induced Senescence / NRIF signals cell death from the nucleus / Activation of BIM and translocation to mitochondria / FCERI mediated MAPK activation / DSCAM interactions / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Activation of the AP-1 family of transcription factors / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Interleukin-38 signaling ...NRAGE signals death through JNK / Oxidative Stress Induced Senescence / NRIF signals cell death from the nucleus / Activation of BIM and translocation to mitochondria / FCERI mediated MAPK activation / DSCAM interactions / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Activation of the AP-1 family of transcription factors / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Interleukin-38 signaling / Activation of BMF and translocation to mitochondria / JUN phosphorylation / regulation of DNA replication origin binding / positive regulation of deacetylase activity / basal dendrite / JUN kinase activity / histone deacetylase regulator activity / positive regulation of protein metabolic process / positive regulation of cyclase activity / neuron development / regulation of macroautophagy / cellular response to amino acid starvation / response to UV / cellular response to cytokine stimulus / positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway / mitogen-activated protein kinase / MAP kinase activity / regulation of DNA-binding transcription factor activity / cellular response to organic substance / regulation of protein localization / response to mechanical stimulus / cellular response to reactive oxygen species / JNK cascade / regulation of circadian rhythm / stress-activated MAPK cascade / cellular response to cadmium ion / negative regulation of protein binding / rhythmic process / histone deacetylase binding / cellular response to mechanical stimulus / Fc-epsilon receptor signaling pathway / peptidyl-threonine phosphorylation / regulation of gene expression / kinase activity / cellular response to lipopolysaccharide / intracellular signal transduction / peptidyl-serine phosphorylation / neuron projection / positive regulation of apoptotic process / axon / protein serine/threonine kinase activity / positive regulation of gene expression / protein phosphorylation / negative regulation of apoptotic process / enzyme binding / mitochondrion / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
MAP kinase signature. / Protein kinase domain / Mitogen-activated protein (MAP) kinase, conserved site / Serine/threonine-protein kinase, active site / Mitogen-activated protein (MAP) kinase, JNK / Protein kinase-like domain superfamily / Protein kinase domain / Serine/Threonine protein kinases active-site signature. / Protein kinase domain profile.
Mitogen-activated protein kinase 8
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å|
|Citation||Journal: 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. / Ready, S. / Rowsell, S. / Su, M. / Toader, D. / Vasbinder, M. / Yu, D. / Yu, Y. / Xue, Y. / Zabludoff, S. / Janetka, J.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
Downloads & links
A: Mitogen-activated protein kinase 8
|#1: Protein/peptide|| |
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
|#3: Chemical|| ChemComp-CFK / ||#4: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.28 Å3/Da / Density % sol: 46.15 %|
|Crystal grow||Temperature: 298 K / Method: evaporation / pH: 7 |
Details: 15% PEG2000 MME, 100 mM HEPES, 10 mM DTT, pH 7, EVAPORATION, temperature 298K
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0159|
|Detector||Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 15, 2000|
|Radiation||Monochromator: Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 1.0159 Å / Relative weight: 1|
|Reflection||Resolution: 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 shell||Resolution: 2→2.11 Å / % possible all: 94.7|
|Refinement||Method 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 |
|Displacement parameters||Biso max: 132.32 Å2 / Biso mean: 37.2244 Å2 / Biso min: 15.02 Å2|
|Refine analyze||Luzzati coordinate error obs: 0.232 Å|
|Refinement step||Cycle: LAST / Resolution: 2→23.33 Å|
|Refine LS restraints|
Refinement-ID: X-RAY DIFFRACTION
|LS refinement shell||Resolution: 2→2.08 Å / Total num. of bins used: 13 |
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi