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Yorodumi- PDB-3zs5: Structural basis for kinase selectivity of three clinical p38alph... -
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-Basic information
Entry | Database: PDB / ID: 3zs5 | ||||||
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Title | Structural basis for kinase selectivity of three clinical p38alpha inhibitors | ||||||
Components | MITOGEN-ACTIVATED PROTEIN KINASE 14MAPK14 | ||||||
Keywords | TRANSFERASE / TAK-715 / SCIO-469 / VX-745 / SB-203580 | ||||||
Function / homology | Function and homology information positive regulation of cyclase activity / stress-activated protein kinase signaling cascade / 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 ...positive regulation of cyclase activity / stress-activated protein kinase signaling cascade / 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 / 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 / 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 dietary excess / response to muramyl dipeptide / RHO GTPases Activate NADPH Oxidases / MAP kinase activity / regulation of ossification / mitogen-activated protein kinase / cellular response to vascular endothelial growth factor stimulus / positive regulation of myoblast differentiation / signal transduction in response to DNA damage / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / stress-activated MAPK cascade / skeletal muscle tissue development / lipopolysaccharide-mediated signaling pathway / positive regulation of cardiac muscle cell proliferation / negative regulation of inflammatory response to antigenic stimulus / 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 / DNA damage checkpoint signaling / activated TAK1 mediates p38 MAPK activation / cellular response to ionizing radiation / stem cell differentiation / positive regulation of glucose import / placenta development / NOD1/2 Signaling Pathway / response to insulin / bone development / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / platelet activation / cellular response to virus / VEGFA-VEGFR2 Pathway / spindle pole / positive regulation of protein import into nucleus / osteoblast differentiation / 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 / peptidyl-serine phosphorylation / protein phosphatase binding / secretory granule lumen / Oxidative Stress Induced Senescence / angiogenesis / Regulation of TP53 Activity through Phosphorylation / cellular response to lipopolysaccharide / 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: 1.6 Å | ||||||
Authors | Azevedo, R. / van Zeeland, M. / Raaijmakers, H.C.A. / Kazemier, B. / Oubrie, A. | ||||||
Citation | Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012 Title: X-ray structure of p38 alpha bound to TAK-715: comparison with three classic inhibitors. Authors: Azevedo, R. / van Zeeland, M. / Raaijmakers, H. / Kazemier, B. / de Vlieg, J. / Oubrie, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zs5.cif.gz | 160.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zs5.ent.gz | 126.5 KB | Display | PDB format |
PDBx/mmJSON format | 3zs5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/3zs5 ftp://data.pdbj.org/pub/pdb/validation_reports/zs/3zs5 | 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: 41494.277 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-360 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMAL-C2X LIKE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA References: UniProt: Q16539, mitogen-activated protein kinase | ||||||
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#2: Chemical | ChemComp-SB2 / | ||||||
#3: Sugar | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | 4-[5-(4-FLUORO-PHENYL)-2-(4-METHANESUL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: HANGING DROP, ROOM TEMP, 20 MM HEPES PH7.1, 50 MM NACL, 10 MM DTT, 5% GLYCEROL, 0.1 G/L METHIONINE, 28% PEG 4K,0.1 M MES PH=6.5, 50 MM N-OCTYL-BETAGLUCOSIDE. CRYOPROTECTANT 28% PEG 4K, 0.1M ...Details: HANGING DROP, ROOM TEMP, 20 MM HEPES PH7.1, 50 MM NACL, 10 MM DTT, 5% GLYCEROL, 0.1 G/L METHIONINE, 28% PEG 4K,0.1 M MES PH=6.5, 50 MM N-OCTYL-BETAGLUCOSIDE. CRYOPROTECTANT 28% PEG 4K, 0.1M MES PH5.9, 50 MM N-OCTYL-BETAGLUCOSIDE, 20% ETHYLENE GLYCOL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 28, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40.7 Å / Num. obs: 44440 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.2 / % possible all: 75.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→51.16 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.941 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LYS 53 SHOWS SOME DISORDER AROUND NZETA AND FORMS A SALTBRIDGE TO GLU71. TWO WATERS NEXT TO LYS53 ARE PROBABLY ONLY PARTLY OCCUPIED. THERE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LYS 53 SHOWS SOME DISORDER AROUND NZETA AND FORMS A SALTBRIDGE TO GLU71. TWO WATERS NEXT TO LYS53 ARE PROBABLY ONLY PARTLY OCCUPIED. THERE IS AN ADDITIONAL HYDROPHOBIC LIGAND IN THE ATP POCKET. I'VE PUT A B-OCTYLGLUCOSIDE INSIDE THOUGH THE GLUCOSIDE PART ISN'T VERY CLEAR. IT COULD BE A SIDE CHAIN FROM THE ACTIVATION LOOP BUT IT DOESN'T MAKE H-BONDS. METHIONINE WOULD BE A BIT SHORT.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.088 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→51.16 Å
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