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Yorodumi- PDB-3mpt: Crystal structure of P38 kinase in complex with a pyrrole-2-carbo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mpt | ||||||
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Title | Crystal structure of P38 kinase in complex with a pyrrole-2-carboxamide inhibitor | ||||||
Components | Mitogen-activated protein kinase 14 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / P38 / SERINE/THREONINE PROTEIN KINASE / MAP KINASE / Pyrrole-2-Carboxamides / inhibitor / TRANSFERASE-TRANSFERASE INHIBIATOR complex / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information stress-activated protein kinase signaling cascade / 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 / cartilage condensation ...stress-activated protein kinase signaling cascade / 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 / cartilage condensation / positive regulation of myoblast fusion / cellular response to UV-B / Platelet sensitization by LDL / mitogen-activated protein kinase p38 binding / positive regulation of muscle cell differentiation / positive regulation of myotube differentiation / NFAT protein binding / Myogenesis / D-glucose import / regulation of cytokine production involved in inflammatory response / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / p38MAPK cascade / Regulation of MITF-M-dependent genes involved in pigmentation / fatty acid oxidation / MAP kinase kinase activity / cellular response to lipoteichoic acid / response to muramyl dipeptide / response to dietary excess / MAP kinase activity / RHO GTPases Activate NADPH Oxidases / regulation of ossification / cellular response to vascular endothelial growth factor stimulus / signal transduction in response to DNA damage / mitogen-activated protein kinase / negative regulation of hippo signaling / positive regulation of myoblast differentiation / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / positive regulation of cardiac muscle cell proliferation / lipopolysaccharide-mediated signaling pathway / stress-activated MAPK cascade / skeletal muscle tissue development / p38MAPK events / striated muscle cell differentiation / response to muscle stretch / positive regulation of interleukin-12 production / positive regulation of brown fat cell differentiation / positive regulation of erythrocyte differentiation / osteoclast differentiation / DNA damage checkpoint signaling / activated TAK1 mediates p38 MAPK activation / positive regulation of D-glucose import / stem cell differentiation / cellular response to ionizing radiation / negative regulation of inflammatory response to antigenic stimulus / NOD1/2 Signaling Pathway / response to insulin / bone development / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / placenta development / cellular response to virus / platelet activation / VEGFA-VEGFR2 Pathway / spindle pole / positive regulation of protein import into nucleus / osteoblast differentiation / ADP signalling through P2Y purinoceptor 1 / chemotaxis / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / cellular senescence / cellular response to tumor necrosis factor / peptidyl-serine phosphorylation / cellular response to lipopolysaccharide / protein phosphatase binding / angiogenesis / secretory granule lumen / Oxidative Stress Induced Senescence / 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 / Neutrophil degranulation / positive regulation of gene expression / regulation of transcription by RNA polymerase II / apoptotic process / 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 / FOURIER SYNTHESIS / Resolution: 1.89 Å | ||||||
Authors | Somers, D.O. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 Title: The discovery and initial optimisation of pyrrole-2-carboxamides as inhibitors of p38alpha MAP kinase. Authors: Down, K. / Bamborough, P. / Alder, C. / Campbell, A. / Christopher, J.A. / Gerelle, M. / Ludbrook, S. / Mallett, D. / Mellor, G. / Miller, D.D. / Pearson, R. / Ray, K. / Solanke, Y. / Somers, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mpt.cif.gz | 92.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mpt.ent.gz | 68.8 KB | Display | PDB format |
PDBx/mmJSON format | 3mpt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/3mpt ftp://data.pdbj.org/pub/pdb/validation_reports/mp/3mpt | HTTPS FTP |
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-Related structure data
Related structure data | 1wfcS S: Starting model for refinement |
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Similar 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: 42650.738 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 / Plasmid: pRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): BRL References: UniProt: Q16539, mitogen-activated protein kinase | ||
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#2: Chemical | ChemComp-1GK / | ||
#3: Chemical | #4: 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: 2.84 Å3/Da / Density % sol: 56.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: See publication for details , pH 6.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 20, 2005 / Details: mirrors |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→62.23 Å / Num. obs: 37532 / % possible obs: 93.8 % / Redundancy: 5.66 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.138 / Χ2: 1 / Net I/σ(I): 7.9 / Scaling rejects: 1608 |
Reflection shell | Resolution: 1.89→1.95 Å / Redundancy: 5.53 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 3.5 / Num. measured all: 19775 / Num. unique all: 3573 / Χ2: 0.99 / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1wfc Resolution: 1.89→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.279 / WRfactor Rwork: 0.217 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.752 / SU B: 5.871 / SU ML: 0.155 / SU R Cruickshank DPI: 0.169 / SU Rfree: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.24 Å2 / Biso mean: 31.085 Å2 / Biso min: 6.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.939 Å / Total num. of bins used: 20
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