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Yorodumi- PDB-2rg6: Phenylalanine pyrrolotriazine p38 alpha map kinase inhibitor comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rg6 | ||||||
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Title | Phenylalanine pyrrolotriazine p38 alpha map kinase inhibitor compound 11J | ||||||
Components | Mitogen-activated protein kinase 14MAPK14 | ||||||
Keywords | TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / KINASE / P38 MAP KINASE | ||||||
Function / homology | Function and homology information positive regulation of cyclase activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / CD163 mediating an anti-inflammatory response / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / KSRP (KHSRP) binds and destabilizes mRNA / DSCAM interactions / cartilage condensation ...positive regulation of cyclase activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / CD163 mediating an anti-inflammatory response / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / KSRP (KHSRP) binds and destabilizes mRNA / DSCAM interactions / cartilage condensation / cellular response to UV-B / Platelet sensitization by LDL / stress-activated protein kinase signaling cascade / mitogen-activated protein kinase p38 binding / positive regulation of myoblast fusion / positive regulation of muscle cell differentiation / negative regulation of hippo signaling / positive regulation of myotube differentiation / NFAT protein binding / Myogenesis / glucose import / response to dietary excess / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / fatty acid oxidation / cellular response to lipoteichoic acid / MAP kinase kinase activity / response to muramyl dipeptide / RHO GTPases Activate NADPH Oxidases / regulation of ossification / MAP kinase activity / mitogen-activated protein kinase / cellular response to vascular endothelial growth factor stimulus / positive regulation of myoblast differentiation / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / stress-activated MAPK cascade / skeletal muscle tissue development / signal transduction in response to DNA damage / lipopolysaccharide-mediated signaling pathway / negative regulation of inflammatory response to antigenic stimulus / positive regulation of cardiac muscle cell proliferation / p38MAPK events / striated muscle cell differentiation / response to muscle stretch / positive regulation of brown fat cell differentiation / positive regulation of interleukin-12 production / osteoclast differentiation / positive regulation of erythrocyte differentiation / placenta development / DNA damage checkpoint signaling / activated TAK1 mediates p38 MAPK activation / cellular response to ionizing radiation / stem cell differentiation / positive regulation of glucose import / negative regulation of canonical Wnt signaling pathway / response to insulin / NOD1/2 Signaling Pathway / bone development / cell morphogenesis / platelet activation / osteoblast differentiation / cellular response to virus / VEGFA-VEGFR2 Pathway / spindle pole / positive regulation of protein import into nucleus / ADP signalling through P2Y purinoceptor 1 / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / chemotaxis / cellular senescence / cellular response to tumor necrosis factor / protein phosphatase binding / peptidyl-serine phosphorylation / angiogenesis / Oxidative Stress Induced Senescence / secretory granule lumen / cellular response to lipopolysaccharide / Regulation of TP53 Activity through Phosphorylation / ficolin-1-rich granule lumen / transcription by RNA polymerase II / cell surface receptor signaling pathway / intracellular signal transduction / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / Neutrophil degranulation / positive regulation of gene expression / regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / nucleoplasm / ATP binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Sack, J.S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: Design, Synthesis, and Anti-inflammatory Properties of Orally Active 4-(Phenylamino)-pyrrolo[2,1-f][1,2,4]triazine p38alpha Mitogen-Activated Protein Kinase Inhibitors Authors: Hynes, J. / Dyckman, A.J. / Lin, S. / Wrobleski, S.T. / Wu, H. / Gillooly, K.M. / Kanner, S.B. / Lonial, H. / Loo, D. / McIntyre, K.W. / Pitt, S. / Shen, D.R. / Shuster, D.J. / Yang, X. / ...Authors: Hynes, J. / Dyckman, A.J. / Lin, S. / Wrobleski, S.T. / Wu, H. / Gillooly, K.M. / Kanner, S.B. / Lonial, H. / Loo, D. / McIntyre, K.W. / Pitt, S. / Shen, D.R. / Shuster, D.J. / Yang, X. / Zhang, R. / Behnia, K. / Zhang, H. / Marathe, P.H. / Doweyko, A.M. / Tokarski, J.S. / Sack, J.S. / Pokross, M. / Kiefer, S.E. / Newitt, J.A. / Barrish, J.C. / Dodd, J. / Schieven, G.L. / Leftheris, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rg6.cif.gz | 89 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rg6.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 2rg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/2rg6 ftp://data.pdbj.org/pub/pdb/validation_reports/rg/2rg6 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42105.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2 / Cell line (production host): BL21 DE3 / Production host: Escherichia coli (E. coli) References: UniProt: Q16539, mitogen-activated protein kinase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.91 % |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å | |||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.72→53.45 Å / Num. obs: 43003 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 23.16 Å2 / Rmerge(I) obs: 0.07 | |||||||||
Reflection shell | Resolution: 1.72→1.78 Å / Redundancy: 6.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→53.45 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 24.19 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→53.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.82 Å / Total num. of bins used: 9
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