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- PDB-5m0d: Structure-based evolution of a hybrid steroid series of Autotaxin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5m0d | |||||||||
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Title | Structure-based evolution of a hybrid steroid series of Autotaxin inhibitors | |||||||||
![]() | Ectonucleotide pyrophosphatase/phosphodiesterase family member 2,Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | |||||||||
![]() | HYDROLASE / medicinal chemistry / structure based design / autotaxin | |||||||||
Function / homology | ![]() response to polycyclic arene / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipase D / phospholipid catabolic process / phosphatidylcholine catabolic process / positive regulation of lamellipodium morphogenesis / lysophospholipase activity / phosphodiesterase I activity / scavenger receptor activity ...response to polycyclic arene / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipase D / phospholipid catabolic process / phosphatidylcholine catabolic process / positive regulation of lamellipodium morphogenesis / lysophospholipase activity / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity / polysaccharide binding / negative regulation of cell-matrix adhesion / positive regulation of oligodendrocyte differentiation / 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 / cellular response to cadmium ion / regulation of cell migration / 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Keune, W.-J. / Heidebrecht, T. / Perrakis, A. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 337.5 KB | Display | ![]() |
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PDB format | ![]() | 271.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5m0eC ![]() 5m0mC ![]() 5m0sC ![]() 2xr9S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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,N410A, L581F, R591T, N806A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q64610, alkylglycerophosphoethanolamine phosphodiesterase |
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#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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 , 8 types, 40 molecules ![](data/chem/img/IOD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/7C8.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/7C8.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-IOD / #4: Chemical | #5: Chemical | ChemComp-CA / | #6: Chemical | ChemComp-7C8 / [ | #7: Chemical | ChemComp-NA / | #8: Chemical | ChemComp-SCN / #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, NaSCN and NH4I |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→75.34 Å / Num. obs: 50000 / % possible obs: 98.3 % / Redundancy: 4.5 % / Net I/σ(I): 41.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2XR9 Resolution: 2.4→75.34 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 37.052 / SU ML: 0.351 / Cross valid method: THROUGHOUT / ESU R: 0.644 / ESU R Free: 0.303 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.659 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→75.34 Å
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Refine LS restraints |
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