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- PDB-8dea: Scaffold Hopping via Ring Opening Enables Identification of Acycl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dea | ||||||
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Title | Scaffold Hopping via Ring Opening Enables Identification of Acyclic Compounds as New Complement Factor D Inhibitors | ||||||
![]() | Complement factor D | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / serine protease inhibitor complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() complement factor D / Alternative complement activation / complement activation, alternative pathway / complement activation / serine-type peptidase activity / platelet alpha granule lumen / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen ...complement factor D / Alternative complement activation / complement activation, alternative pathway / complement activation / serine-type peptidase activity / platelet alpha granule lumen / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Raman, K. / Babu, Y.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Scaffold hopping via ring opening enables identification of acyclic compounds as new complement Factor D inhibitors. Authors: Zhang, W. / Wu, M. / Vadlakonda, S. / Juarez, L. / Cheng, X. / Muppa, S. / Chintareddy, V. / Vogeti, L. / Kellogg-Yelder, D. / Williams, J. / Polach, K. / Chen, X. / Raman, K. / Babu, Y.S. / Kotian, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182.1 KB | Display | ![]() |
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PDB format | ![]() | 139 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 33.8 KB | Display | |
Data in CIF | ![]() | 44.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8d95C ![]() 8dg6C ![]() 1dicS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24596.965 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | ChemComp-R7X / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.25 % / Description: square blocks |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: peg4k 25% , 0.1M MES 5.8 buffer / PH range: 6.4 |
-Data collection
Diffraction | Mean temperature: 170 K / Ambient temp details: cryostream / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 36438 / % possible obs: 74.5 % / Redundancy: 3.2 % / CC1/2: 0.771 / CC star: 0.993 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.311 / Χ2: 0.861 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 1.6 % / Num. unique obs: 1919 / CC1/2: 0.771 / CC star: 0.923 / Χ2: 0.532 / % possible all: 46.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1dic Resolution: 2.214→46.46 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.879 / WRfactor Rfree: 0.281 / WRfactor Rwork: 0.213 / SU B: 9.716 / SU ML: 0.238 / Average fsc free: 0.9334 / Average fsc work: 0.9623 / Cross valid method: FREE R-VALUE / ESU R: 0.557 / ESU R Free: 0.321 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.495 Å2
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Refinement step | Cycle: LAST / Resolution: 2.214→46.46 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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