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Yorodumi- PDB-4yt6: Factor VIIa in complex with the inhibitor 4-{[(R)-[5-ethoxy-2-flu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yt6 | |||||||||
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Title | Factor VIIa in complex with the inhibitor 4-{[(R)-[5-ethoxy-2-fluoro-3-(propan-2-yloxy)phenyl](4-phenyl-1H-imidazol-2-yl)methyl]amino}benzenecarboximidamide | |||||||||
Components | (Coagulation factor VII ...) x 2 | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / glycoprotein / hydrolase / serine protease / plasma / blood coagulation factor / protein inhibitor complex / calcium-binding / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide ...coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide / response to thyroxine / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / positive regulation of blood coagulation / animal organ regeneration / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Removal of aminoterminal propeptides from gamma-carboxylated proteins / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / protein processing / Golgi lumen / circadian rhythm / response to estrogen / blood coagulation / response to estradiol / collagen-containing extracellular matrix / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / extracellular space / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | |||||||||
Authors | Wei, A. | |||||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2015 Title: Design and synthesis of potent, selective phenylimidazole-based FVIIa inhibitors. Authors: Glunz, P.W. / Cheng, X. / Cheney, D.L. / Weigelt, C.A. / Wei, A. / Luettgen, J.M. / Wong, P.C. / Wexler, R.R. / Priestley, E.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yt6.cif.gz | 88.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yt6.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 4yt6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yt6_validation.pdf.gz | 790.3 KB | Display | wwPDB validaton report |
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Full document | 4yt6_full_validation.pdf.gz | 792.1 KB | Display | |
Data in XML | 4yt6_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 4yt6_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/4yt6 ftp://data.pdbj.org/pub/pdb/validation_reports/yt/4yt6 | HTTPS FTP |
-Related structure data
Related structure data | 4yt7C 1danS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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
-Coagulation factor VII ... , 2 types, 2 molecules HL
#1: Protein | Mass: 28103.256 Da / Num. of mol.: 1 / Fragment: UNP residues 213-466 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Production host: Cricetinae (hamsters) / References: UniProt: P08709, coagulation factor VIIa |
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#2: Protein | Mass: 6272.113 Da / Num. of mol.: 1 / Fragment: UNP residues 148-204 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Production host: Cricetinae (hamsters) / References: UniProt: P08709, coagulation factor VIIa |
-Non-polymers , 5 types, 310 molecules
#3: Chemical | ChemComp-4JY / | ||||
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#4: Chemical | ChemComp-CA / | ||||
#5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.89 Å3/Da / Density % sol: 68.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM MES, pH 6.0, 20 mM calcium chloride, 17.5% w/v PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 26, 2004 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→50 Å / Num. all: 33799 / Num. obs: 31050 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 31.33 Å2 / Rsym value: 0.074 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 2.07→2.14 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 6.8 / Rejects: 0 / % possible all: 76.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1DAN Resolution: 2.07→26.16 Å / Cor.coef. Fo:Fc: 0.9437 / Cor.coef. Fo:Fc free: 0.9298 / SU R Cruickshank DPI: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.16 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.132
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Displacement parameters | Biso max: 123.57 Å2 / Biso mean: 34.94 Å2 / Biso min: 14.92 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.07→26.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.07→2.14 Å / Total num. of bins used: 15
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