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- PDB-5lz8: Fragment-based inhibitors of Lipoprotein associated Phospholipase A2 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lz8 | ||||||
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Title | Fragment-based inhibitors of Lipoprotein associated Phospholipase A2 | ||||||
![]() | Platelet-activating factor acetylhydrolase | ||||||
![]() | HYDROLASE / Lp-PLA2 phospholipase / lipid metabolism / inhibitors | ||||||
Function / homology | ![]() plasma lipoprotein particle oxidation / platelet activating factor catabolic process / calcium-independent phospholipase A2 activity / 1-alkyl-2-acetylglycerophosphocholine esterase / platelet activating factor metabolic process / 1-alkyl-2-acetylglycerophosphocholine esterase activity / lipid oxidation / phosphatidylcholine catabolic process / low-density lipoprotein particle / high-density lipoprotein particle ...plasma lipoprotein particle oxidation / platelet activating factor catabolic process / calcium-independent phospholipase A2 activity / 1-alkyl-2-acetylglycerophosphocholine esterase / platelet activating factor metabolic process / 1-alkyl-2-acetylglycerophosphocholine esterase activity / lipid oxidation / phosphatidylcholine catabolic process / low-density lipoprotein particle / high-density lipoprotein particle / low-density lipoprotein particle remodeling / positive regulation of monocyte chemotaxis / peptide hormone processing / hydrolase activity, acting on ester bonds / Synthesis, secretion, and deacylation of Ghrelin / phospholipid binding / positive regulation of inflammatory response / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Woolford, A. / Day, P. | ||||||
![]() | ![]() Title: Fragment-Based Approach to the Development of an Orally Bioavailable Lactam Inhibitor of Lipoprotein-Associated Phospholipase A2 (Lp-PLA2). Authors: Woolford, A.J. / Day, P.J. / Beneton, V. / Berdini, V. / Coyle, J.E. / Dudit, Y. / Grondin, P. / Huet, P. / Lee, L.Y. / Manas, E.S. / McMenamin, R.L. / Murray, C.W. / Page, L.W. / Patel, V.K. ...Authors: Woolford, A.J. / Day, P.J. / Beneton, V. / Berdini, V. / Coyle, J.E. / Dudit, Y. / Grondin, P. / Huet, P. / Lee, L.Y. / Manas, E.S. / McMenamin, R.L. / Murray, C.W. / Page, L.W. / Patel, V.K. / Potvain, F. / Rich, S.J. / Sang, Y. / Somers, D.O. / Trottet, L. / Wan, Z. / Zhang, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.7 KB | Display | ![]() |
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PDB format | ![]() | 132.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 673.6 KB | Display | ![]() |
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Full document | ![]() | 675.3 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lyyC ![]() 5lz2C ![]() 5lz4C ![]() 5lz5C ![]() 5lz7C ![]() 5lz9C 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 44203.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q13093, 1-alkyl-2-acetylglycerophosphocholine esterase | ||||
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#2: Chemical | #3: Chemical | ChemComp-7BP / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 28.0%w/v PEG 3350, 0.1M HEPES/NaOHpH=7.4, 1.3M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 15, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→42.38 Å / Num. obs: 22893 / % possible obs: 98 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.11→2.19 Å / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 1.8 / % possible all: 92.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 36.07 Å2
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Refinement step | Cycle: 1 / Resolution: 2.11→42.38 Å
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Refine LS restraints |
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