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Yorodumi- PDB-6qmr: Complement factor D in complex with the inhibitor (S)-2-(2-((3'-(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qmr | ||||||
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Title | Complement factor D in complex with the inhibitor (S)-2-(2-((3'-(1-amino-2-hydroxyethyl)-[1,1'-biphenyl]-3-yl)methoxy)phenyl)acetic acid | ||||||
Components | Complement factor D | ||||||
Keywords | HYDROLASE / Complement factor D / inhibitor | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Karki, R. / Powers, J. / Mainolfi, N. / Anderson, K. / Belanger, D. / Liu, D. / Jendza, K. / Gelin, C.F. / Solovay, C. / Mac Sweeeny, A. ...Karki, R. / Powers, J. / Mainolfi, N. / Anderson, K. / Belanger, D. / Liu, D. / Jendza, K. / Gelin, C.F. / Solovay, C. / Mac Sweeeny, A. / Delgado, O. / Crowley, M. / Liao, S.-M. / Argikar, U.A. / Flohr, S. / La Bonte, L.R. / Lorthiois, E.L. / Vulpetti, A. / Cumin, F. / Brown, A. / Adams, C. / Jaffee, B. / Mogi, M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2019 Title: Design, Synthesis, and Preclinical Characterization of Selective Factor D Inhibitors Targeting the Alternative Complement Pathway. Authors: Karki, R.G. / Powers, J. / Mainolfi, N. / Anderson, K. / Belanger, D.B. / Liu, D. / Ji, N. / Jendza, K. / Gelin, C.F. / Mac Sweeney, A. / Solovay, C. / Delgado, O. / Crowley, M. / Liao, S.M. ...Authors: Karki, R.G. / Powers, J. / Mainolfi, N. / Anderson, K. / Belanger, D.B. / Liu, D. / Ji, N. / Jendza, K. / Gelin, C.F. / Mac Sweeney, A. / Solovay, C. / Delgado, O. / Crowley, M. / Liao, S.M. / Argikar, U.A. / Flohr, S. / La Bonte, L.R. / Lorthiois, E.L. / Vulpetti, A. / Brown, A. / Long, D. / Prentiss, M. / Gradoux, N. / de Erkenez, A. / Cumin, F. / Adams, C. / Jaffee, B. / Mogi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qmr.cif.gz | 276.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qmr.ent.gz | 223.5 KB | Display | PDB format |
PDBx/mmJSON format | 6qmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qmr_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 6qmr_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 6qmr_validation.xml.gz | 51 KB | Display | |
Data in CIF | 6qmr_validation.cif.gz | 69.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/6qmr ftp://data.pdbj.org/pub/pdb/validation_reports/qm/6qmr | HTTPS FTP |
-Related structure data
Related structure data | 6qmtC 1dsuS 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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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 27097.936 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CFD, DF, PFD / Production host: Escherichia coli (E. coli) / References: UniProt: P00746, complement factor D #2: Chemical | ChemComp-J6T / #3: 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: 1.99 Å3/Da / Density % sol: 38.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG MME 2000, 0.1M sodium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→57.9 Å / Num. obs: 142642 / % possible obs: 84.5 % / Observed criterion σ(F): -3 / Redundancy: 1.73 % / CC1/2: 0.996 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.102 / Net I/σ(I): 5.82 |
Reflection shell | Resolution: 1.54→1.63 Å / Redundancy: 1.59 % / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 21044 / CC1/2: 0.381 / Rrim(I) all: 1.18 / % possible all: 77.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1dsu Resolution: 2→49.23 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.346 / ESU R Free: 0.225 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: 117.17 Å2 / Biso mean: 21.421 Å2 / Biso min: 3 Å2
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Refinement step | Cycle: final / Resolution: 2→49.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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