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Yorodumi- PDB-5ow8: Indole-2 carboxamides as selective secreted phospholipase A2 type... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ow8 | ||||||
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Title | Indole-2 carboxamides as selective secreted phospholipase A2 type X (sPLA2-X) inhibitors | ||||||
Components | Group 10 secretory phospholipase A2 | ||||||
Keywords | LIPID BINDING PROTEIN / Inhibitor / secreted / phospholipase | ||||||
Function / homology | Function and homology information phosphatidylserine metabolic process / lysophospholipid transport / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / production of molecular mediator involved in inflammatory response / platelet activating factor catabolic process / positive regulation of acrosome reaction / Acyl chain remodelling of PG / intestinal stem cell homeostasis / phospholipase activity ...phosphatidylserine metabolic process / lysophospholipid transport / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / production of molecular mediator involved in inflammatory response / platelet activating factor catabolic process / positive regulation of acrosome reaction / Acyl chain remodelling of PG / intestinal stem cell homeostasis / phospholipase activity / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / 1-alkyl-2-acetylglycerophosphocholine esterase activity / Synthesis of PA / negative regulation of cholesterol efflux / arachidonic acid metabolic process / phosphatidylglycerol metabolic process / calcium-dependent phospholipase A2 activity / phosphatidylcholine catabolic process / positive regulation of prostaglandin secretion / positive regulation of macrophage derived foam cell differentiation / phosphatidylcholine metabolic process / positive regulation of lipid storage / macrophage activation / positive regulation of arachidonic acid secretion / low-density lipoprotein particle remodeling / fertilization / phospholipase A2 / phospholipase A2 activity / prostaglandin biosynthetic process / regulation of macrophage activation / arachidonic acid secretion / hair follicle morphogenesis / erythrocyte maturation / negative regulation of cytokine production involved in inflammatory response / phospholipid metabolic process / positive regulation of protein metabolic process / cellular response to leukemia inhibitory factor / acrosomal vesicle / cholesterol homeostasis / axon guidance / phospholipid binding / negative regulation of DNA-binding transcription factor activity / negative regulation of inflammatory response / defense response to virus / lysosome / calcium ion binding / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Sandmark, J.S. / Roth, R.G. / Knerr, L. / Bodin, C. / Pettersen, D. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2018 Title: Discovery of a Series of Indole-2 Carboxamides as Selective Secreted Phospholipase A2Type X (sPLA2-X) Inhibitors. Authors: Knerr, L. / Giordanetto, F. / Nordberg, P. / Pettersen, D. / Selmi, N. / Beisel, H.G. / de la Motte, H. / Olsson, T. / Perkins, T.D.J. / Herslof, M. / Mansson, A. / Dahlstrom, M. / Starke, I. ...Authors: Knerr, L. / Giordanetto, F. / Nordberg, P. / Pettersen, D. / Selmi, N. / Beisel, H.G. / de la Motte, H. / Olsson, T. / Perkins, T.D.J. / Herslof, M. / Mansson, A. / Dahlstrom, M. / Starke, I. / Broddefalk, J. / Saarinen, G. / Klingegard, F. / Hurt-Camejo, E. / Rosengren, B. / Brengdahl, J. / Jansen, F. / Rohman, M. / Sandmark, J. / Hallberg, K. / Akerud, T. / Roth, R.G. / Ahlqvist, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ow8.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ow8.ent.gz | 49.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ow8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/5ow8 ftp://data.pdbj.org/pub/pdb/validation_reports/ow/5ow8 | 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 13644.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G10 / Plasmid: pET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: O15496, phospholipase A2 |
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-Non-polymers , 6 types, 128 molecules
#2: Chemical | #3: Chemical | ChemComp-DMS / #4: Chemical | #5: Chemical | ChemComp-PEG / #6: Chemical | ChemComp-CL / #7: 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: 2.23 Å3/Da / Density % sol: 44.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 37-45% PEG400 0.1M bis-Tris pH 5.6-5.9 / PH range: 5.6-5.9 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Mar 9, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→44.083 Å / Num. obs: 19430 / % possible obs: 97.1 % / Redundancy: 5.5 % / Rpim(I) all: 0.069 / Rrim(I) all: 0.166 / Rsym value: 0.15 / Net I/av σ(I): 4.2 / Net I/σ(I): 7.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.898 / SU B: 4.589 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.179 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 55.74 Å2 / Biso mean: 23.132 Å2 / Biso min: 13.51 Å2
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Refinement step | Cycle: final / Resolution: 1.9→44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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