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Yorodumi- PDB-2ojg: Crystal structure of ERK2 in complex with N,N-dimethyl-4-(4-pheny... -
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-Basic information
Entry | Database: PDB / ID: 2ojg | ||||||
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Title | Crystal structure of ERK2 in complex with N,N-dimethyl-4-(4-phenyl-1H-pyrazol-3-yl)-1H-pyrrole-2-carboxamide | ||||||
Components | Mitogen-activated protein kinase 1 | ||||||
Keywords | TRANSFERASE / kinase inhibitor | ||||||
Function / homology | Function and homology information phospho-PLA2 pathway / Signaling by MAPK mutants / Suppression of apoptosis / RAF-independent MAPK1/3 activation / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / ERKs are inactivated ...phospho-PLA2 pathway / Signaling by MAPK mutants / Suppression of apoptosis / RAF-independent MAPK1/3 activation / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / ERKs are inactivated / response to epidermal growth factor / Signaling by MAP2K mutants / Signaling by NODAL / RSK activation / Golgi Cisternae Pericentriolar Stack Reorganization / regulation of cellular pH / positive regulation of macrophage proliferation / outer ear morphogenesis / Regulation of the apoptosome activity / regulation of Golgi inheritance / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / regulation of early endosome to late endosome transport / Negative feedback regulation of MAPK pathway / regulation of cytoskeleton organization / regulation of stress-activated MAPK cascade / IFNG signaling activates MAPKs / Frs2-mediated activation / positive regulation of macrophage chemotaxis / response to exogenous dsRNA / lung morphogenesis / ERBB2-ERBB3 signaling pathway / face development / Recycling pathway of L1 / Activation of the AP-1 family of transcription factors / androgen receptor signaling pathway / ERK/MAPK targets / RUNX2 regulates osteoblast differentiation / pseudopodium / progesterone receptor signaling pathway / positive regulation of telomere capping / MAPK1 (ERK2) activation / negative regulation of cell differentiation / Bergmann glial cell differentiation / thyroid gland development / Advanced glycosylation endproduct receptor signaling / steroid hormone mediated signaling pathway / RHO GTPases Activate NADPH Oxidases / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Regulation of HSF1-mediated heat shock response / RHO GTPases Activate WASPs and WAVEs / regulation of ossification / MAP kinase activity / phosphatase binding / mitogen-activated protein kinase / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / Nuclear events stimulated by ALK signaling in cancer / stress-activated MAPK cascade / Schwann cell development / Growth hormone receptor signaling / lipopolysaccharide-mediated signaling pathway / positive regulation of telomerase activity / ERK1 and ERK2 cascade / cellular response to cadmium ion / positive regulation of telomere maintenance via telomerase / cellular response to amino acid starvation / myelination / NPAS4 regulates expression of target genes / NCAM signaling for neurite out-growth / phosphotyrosine residue binding / RNA polymerase II CTD heptapeptide repeat kinase activity / ESR-mediated signaling / insulin-like growth factor receptor signaling pathway / thymus development / positive regulation of peptidyl-threonine phosphorylation / response to nicotine / Regulation of PTEN gene transcription / Signal transduction by L1 / long-term synaptic potentiation / caveola / Negative regulation of FGFR3 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR2 signaling / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / B cell receptor signaling pathway / Spry regulation of FGF signaling / peptidyl-threonine phosphorylation / Signaling by high-kinase activity BRAF mutants / regulation of protein stability / MAP2K and MAPK activation / Oncogene Induced Senescence / mitotic spindle / Regulation of actin dynamics for phagocytic cup formation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Xie, X. / Jacobs, M.D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2007 Title: Flipped Out: Structure-Guided Design of Selective Pyrazolylpyrrole ERK Inhibitors. Authors: Aronov, A.M. / Baker, C. / Bemis, G.W. / Cao, J. / Chen, G. / Ford, P.J. / Germann, U.A. / Green, J. / Hale, M.R. / Jacobs, M. / Janetka, J.W. / Maltais, F. / Martinez-Botella, G. / Namchuk, ...Authors: Aronov, A.M. / Baker, C. / Bemis, G.W. / Cao, J. / Chen, G. / Ford, P.J. / Germann, U.A. / Green, J. / Hale, M.R. / Jacobs, M. / Janetka, J.W. / Maltais, F. / Martinez-Botella, G. / Namchuk, M.N. / Straub, J. / Tang, Q. / Xie, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ojg.cif.gz | 88 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ojg.ent.gz | 65 KB | Display | PDB format |
PDBx/mmJSON format | 2ojg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/2ojg ftp://data.pdbj.org/pub/pdb/validation_reports/oj/2ojg | 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: 43616.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK1, ERK2, PRKM1 / Plasmid: pT7Blue / Production host: Escherichia coli (E. coli) References: UniProt: P28482, mitogen-activated protein kinase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-19A / |
#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: 2.24 Å3/Da / Density % sol: 45.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.2 Details: protein: 14 mg/ml, 20 mM Tris, pH 7.0, 5 mM DTT, 200 mM NaCl. precipitant: 100 mM HEPES, pH 7.2, 28-30% PEG-MME-2000, 200 mM Ammonium Sulfate, 20 mM 2-ME, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 23772 / % possible obs: 93.1 % / Redundancy: 2.77 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 14.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→19.97 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 766664.688 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.4 Å2 / ksol: 0.349 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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