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Yorodumi- PDB-4obp: MAP4K4 in complex with inhibitor (compound 29), 6-(2-FLUOROPYRIDI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4obp | ||||||
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Title | MAP4K4 in complex with inhibitor (compound 29), 6-(2-FLUOROPYRIDIN-4-YL)PYRIDO[3,2-D]PYRIMIDIN-4-AMINE | ||||||
Components | Mitogen-activated protein kinase kinase kinase kinase 4 | ||||||
Keywords | transferase/transferase inhibitor / kinase / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information positive regulation of ARF protein signal transduction / creatine kinase activity / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / negative regulation of cell-matrix adhesion / positive regulation of focal adhesion assembly / regulation of MAPK cascade / regulation of JNK cascade / neuron projection morphogenesis / positive regulation of GTPase activity ...positive regulation of ARF protein signal transduction / creatine kinase activity / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / negative regulation of cell-matrix adhesion / positive regulation of focal adhesion assembly / regulation of MAPK cascade / regulation of JNK cascade / neuron projection morphogenesis / positive regulation of GTPase activity / MAPK cascade / microtubule binding / Oxidative Stress Induced Senescence / non-specific serine/threonine protein kinase / intracellular signal transduction / positive regulation of cell migration / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / negative regulation of apoptotic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.27 Å | ||||||
Authors | Harris, S.F. / Wu, P. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Discovery of Selective 4-Amino-pyridopyrimidine Inhibitors of MAP4K4 Using Fragment-Based Lead Identification and Optimization. Authors: Crawford, T.D. / Ndubaku, C.O. / Chen, H. / Boggs, J.W. / Bravo, B.J. / Delatorre, K. / Giannetti, A.M. / Gould, S.E. / Harris, S.F. / Magnuson, S.R. / McNamara, E. / Murray, L.J. / ...Authors: Crawford, T.D. / Ndubaku, C.O. / Chen, H. / Boggs, J.W. / Bravo, B.J. / Delatorre, K. / Giannetti, A.M. / Gould, S.E. / Harris, S.F. / Magnuson, S.R. / McNamara, E. / Murray, L.J. / Nonomiya, J. / Sambrone, A. / Schmidt, S. / Smyczek, T. / Stanley, M. / Vitorino, P. / Wang, L. / West, K. / Wu, P. / Ye, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4obp.cif.gz | 137.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4obp.ent.gz | 106.2 KB | Display | PDB format |
PDBx/mmJSON format | 4obp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/4obp ftp://data.pdbj.org/pub/pdb/validation_reports/ob/4obp | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 37870.078 Da / Num. of mol.: 2 / Fragment: kinase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HGK, KIAA0687, MAP4K4, NIK / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: O95819, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-MES / | #4: Chemical | ChemComp-2QU / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.64 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: 0.2 M potassium citrate pH 8.3, 20% PEG 3350, vapor diffusion, sitting drop, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 7 % / Av σ(I) over netI: 13.4 / Number: 216377 / Rsym value: 0.045 / D res high: 2.268 Å / D res low: 91.218 Å / Num. obs: 30881 / % possible obs: 99.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.27→91.2 Å / Num. obs: 30881 / % possible obs: 99.9 % |
-Phasing
Phasing | Method: molecular replacement |
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Phasing MR | Packing: 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→60.27 Å / Cor.coef. Fo:Fc: 0.9385 / Cor.coef. Fo:Fc free: 0.9241 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.321 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso max: 156.19 Å2 / Biso mean: 51.3589 Å2 / Biso min: 18.58 Å2
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Refine analyze | Luzzati coordinate error obs: 0.306 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→60.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.27→2.35 Å / Total num. of bins used: 15
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