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Yorodumi- PDB-5m0m: Structure-based evolution of a hybrid steroid series of Autotaxin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m0m | |||||||||
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Title | Structure-based evolution of a hybrid steroid series of Autotaxin inhibitors | |||||||||
Components | Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | |||||||||
Keywords | HYDROLASE / medicinal chemistry / structure based design / autotaxin | |||||||||
Function / homology | Function and homology information response to polycyclic arene / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipid catabolic process / phosphatidylcholine catabolic process / lysophospholipase activity / positive regulation of lamellipodium morphogenesis / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity ...response to polycyclic arene / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipid catabolic process / phosphatidylcholine catabolic process / lysophospholipase activity / positive regulation of lamellipodium morphogenesis / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity / polysaccharide binding / positive regulation of oligodendrocyte differentiation / negative regulation of cell-matrix adhesion / positive regulation of epithelial cell migration / positive regulation of focal adhesion assembly / estrous cycle / phospholipid metabolic process / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / cellular response to cadmium ion / cell chemotaxis / cellular response to estradiol stimulus / positive regulation of peptidyl-tyrosine phosphorylation / nucleic acid binding / immune response / calcium ion binding / positive regulation of cell population proliferation / extracellular space / zinc ion binding Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Keune, W.-J. / Heidebrecht, T. / Perrakis, A. | |||||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Rational Design of Autotaxin Inhibitors by Structural Evolution of Endogenous Modulators. Authors: Keune, W.J. / Potjewyd, F. / Heidebrecht, T. / Salgado-Polo, F. / Macdonald, S.J. / Chelvarajan, L. / Abdel Latif, A. / Soman, S. / Morris, A.J. / Watson, A.J. / Jamieson, C. / Perrakis, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m0m.cif.gz | 341.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m0m.ent.gz | 271.8 KB | Display | PDB format |
PDBx/mmJSON format | 5m0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/5m0m ftp://data.pdbj.org/pub/pdb/validation_reports/m0/5m0m | HTTPS FTP |
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-Related structure data
Related structure data | 5m0dC 5m0eC 5m0sC 2xr9S 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 95037.656 Da / Num. of mol.: 1 / Mutation: N410A, L581F, R591T, N806A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Enpp2, Atx, Npps2 / Cell line (production host): HEK293 / Organ (production host): kidney / Production host: Homo sapiens (human) References: UniProt: Q64610, alkylglycerophosphoethanolamine phosphodiesterase |
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#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 9 types, 124 molecules
#3: Chemical | ChemComp-IOD / #4: Chemical | #5: Chemical | ChemComp-CA / | #6: Chemical | ChemComp-7CF / [ | #7: Chemical | #8: Chemical | ChemComp-SCN / #9: Chemical | ChemComp-GOL / #10: Chemical | ChemComp-NKP / ( | #11: 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: 2.22 Å3/Da / Density % sol: 44.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, NaSCN and NH4I |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→75.27 Å / Num. obs: 45214 / % possible obs: 89.2 % / Redundancy: 27 % / Net I/σ(I): 19.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XR9 Resolution: 2.1→75.27 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 16.548 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.205 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.019 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→75.27 Å
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