+Open data
-Basic information
Entry | Database: PDB / ID: 4u43 | ||||||
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Title | MAP4K4 in complex with inhibitor (compound 6) | ||||||
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 / Resolution: 2.18 Å | ||||||
Authors | Harris, S.F. / Wu, P. / Coons, M. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2014 Title: Fragment-based identification and optimization of a class of potent pyrrolo[2,1-f][1,2,4]triazine MAP4K4 inhibitors. Authors: Wang, L. / Stanley, M. / Boggs, J.W. / Crawford, T.D. / Bravo, B.J. / Giannetti, A.M. / Harris, S.F. / Magnuson, S.R. / Nonomiya, J. / Schmidt, S. / Wu, P. / Ye, W. / Gould, S.E. / Murray, L. ...Authors: Wang, L. / Stanley, M. / Boggs, J.W. / Crawford, T.D. / Bravo, B.J. / Giannetti, A.M. / Harris, S.F. / Magnuson, S.R. / Nonomiya, J. / Schmidt, S. / Wu, P. / Ye, W. / Gould, S.E. / Murray, L.J. / Ndubaku, C.O. / Chen, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u43.cif.gz | 136.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u43.ent.gz | 105.5 KB | Display | PDB format |
PDBx/mmJSON format | 4u43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/4u43 ftp://data.pdbj.org/pub/pdb/validation_reports/u4/4u43 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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 (UNP residues 2-328) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP4K4, HGK, KIAA0687, NIK / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 References: UniProt: O95819, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-3D8 / | #3: 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: 2.06 Å3/Da / Density % sol: 40.19 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1001 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: KOHZU Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1001 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.18→50 Å / Num. obs: 33286 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 47.76 Å2 / Rmerge(I) obs: 0.064 / Χ2: 1.034 / Net I/av σ(I): 26.119 / Net I/σ(I): 9.3 / Num. measured all: 203453 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Resolution: 2.18→29.08 Å / SU R Cruickshank DPI: 0.263 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.27 / SU Rfree Blow DPI: 0.204 / SU Rfree Cruickshank DPI: 0.205
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Displacement parameters | Biso max: 156.08 Å2 / Biso mean: 58.13 Å2 / Biso min: 27.13 Å2
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Refine analyze | Luzzati coordinate error obs: 0.289 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.18→29.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.18→2.25 Å / Total num. of bins used: 17
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