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Yorodumi- PDB-3cgf: IRAK-4 Inhibitors (Part II)- A structure based assessment of imid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cgf | ||||||
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Title | IRAK-4 Inhibitors (Part II)- A structure based assessment of imidazo[1,2 a]pyridine binding | ||||||
Components | Mitogen-activated protein kinase 10 | ||||||
Keywords | TRANSFERASE / kinase two-lobed structure / Alternative splicing / ATP-binding / Chromosomal rearrangement / Cytoplasm / Epilepsy / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase | ||||||
Function / homology | Function and homology information JUN kinase activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / response to light stimulus / mitogen-activated protein kinase / JNK cascade / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / FCERI mediated MAPK activation / regulation of circadian rhythm ...JUN kinase activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / response to light stimulus / mitogen-activated protein kinase / JNK cascade / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / FCERI mediated MAPK activation / regulation of circadian rhythm / cellular senescence / rhythmic process / Oxidative Stress Induced Senescence / protein phosphorylation / protein serine kinase activity / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Ceska, T.A. / Platt, A. / Fortunato, M. / Dickson, K.M. / Buckley, G. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2008 Title: IRAK-4 inhibitors. Part II: A structure-based assessment of imidazo[1,2-a]pyridine binding Authors: Buckley, G.M. / Ceska, T.A. / Fraser, J.L. / Gowers, L. / Groom, C.R. / Higueruelo, A.P. / Jenkins, K. / Mack, S.R. / Morgan, T. / Parry, D.M. / Pitt, W.R. / Rausch, O. / Richard, M.D. / Sabin, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cgf.cif.gz | 83.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cgf.ent.gz | 62.1 KB | Display | PDB format |
PDBx/mmJSON format | 3cgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cgf_validation.pdf.gz | 804.7 KB | Display | wwPDB validaton report |
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Full document | 3cgf_full_validation.pdf.gz | 815.7 KB | Display | |
Data in XML | 3cgf_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 3cgf_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/3cgf ftp://data.pdbj.org/pub/pdb/validation_reports/cg/3cgf | HTTPS FTP |
-Related structure data
Related structure data | 3cgoC 1jnkS S: Starting model for refinement C: citing same article (ref.) |
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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: 42116.727 Da / Num. of mol.: 1 / Fragment: Protein kinase domain, UNP residues 40-402 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK10, JNK3, JNK3A, PRKM10 / Production host: Escherichia coli (E. coli) References: UniProt: P53779, mitogen-activated protein kinase |
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#2: Chemical | ChemComp-JNF / |
-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: 47.9 % |
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Crystal grow | pH: 7 / Details: pH7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 18, 2005 / Details: OSMIC |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 8488 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.95 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 3→3.05 Å / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.4 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JNK Resolution: 3→18 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 999999 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 12 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→18 Å
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Refine LS restraints |
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Xplor file |
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