+Open data
-Basic information
Entry | Database: PDB / ID: 2f9b | ||||||
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Title | Discovery of Novel Heterocyclic Factor VIIa Inhibitors | ||||||
Components |
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Keywords | HYDROLASE/BLOOD CLOTTING / serine protease / short hydrogen bond / active site-directed inhibitor / HYDROLASE-BLOOD CLOTTING COMPLEX | ||||||
Function / homology | Function and homology information activation of blood coagulation via clotting cascade / activation of plasma proteins involved in acute inflammatory response / 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 ...activation of blood coagulation via clotting cascade / activation of plasma proteins involved in acute inflammatory response / 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 / NGF-stimulated transcription / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / cytokine receptor activity / 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 / positive regulation of endothelial cell proliferation / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / positive regulation of interleukin-8 production / protein processing / phospholipid binding / cytokine-mediated signaling pathway / Golgi lumen / circadian rhythm / response to estrogen / positive regulation of angiogenesis / activation of cysteine-type endopeptidase activity involved in apoptotic process / blood coagulation / response to estradiol / collagen-containing extracellular matrix / protease binding / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of gene expression / cell surface / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å | ||||||
Authors | Rai, R. / Kolesnikov, A. / Sprengeler, P.A. / Torkelson, S. / Ton, T. / Katz, B.A. / Yu, C. / Hendrix, J. / Shrader, W.D. / Stephens, R. ...Rai, R. / Kolesnikov, A. / Sprengeler, P.A. / Torkelson, S. / Ton, T. / Katz, B.A. / Yu, C. / Hendrix, J. / Shrader, W.D. / Stephens, R. / Cabuslay, R. / Sanford, E. / Young, W.B. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2006 Title: Discovery of novel heterocyclic factor VIIa inhibitors. Authors: Rai, R. / Kolesnikov, A. / Sprengeler, P.A. / Torkelson, S. / Ton, T. / Katz, B.A. / Yu, C. / Hendrix, J. / Shrader, W.D. / Stephens, R. / Cabuslay, R. / Sanford, E. / Young, W.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f9b.cif.gz | 121.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f9b.ent.gz | 90.1 KB | Display | PDB format |
PDBx/mmJSON format | 2f9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f9b_validation.pdf.gz | 724.2 KB | Display | wwPDB validaton report |
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Full document | 2f9b_full_validation.pdf.gz | 744.6 KB | Display | |
Data in XML | 2f9b_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 2f9b_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/2f9b ftp://data.pdbj.org/pub/pdb/validation_reports/f9/2f9b | HTTPS FTP |
-Related structure data
Related structure data | 1danS 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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Details | The biological assembly is contained in the asymmetic unit (factor VIIa light chain, factor VIIa heavy chain, soluble tissue factor, and the inhibitor) |
-Components
#1: Protein | Mass: 17046.975 Da / Num. of mol.: 1 / Fragment: light chain, residues 61-212 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Cell line (production host): embryonic kidney cell line 293 / Production host: Homo sapiens (human) / References: UniProt: P08709, coagulation factor VIIa |
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#2: Protein | Mass: 28103.256 Da / Num. of mol.: 1 / Fragment: heavy chain, residues 213-466 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Cell line (production host): embryonic kidney cell line 293 / Production host: Homo sapiens (human) / References: UniProt: P08709, coagulation factor VIIa |
#3: Protein | Mass: 24739.434 Da / Num. of mol.: 1 / Fragment: residues 34-251 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F3 / Plasmid: PET-21A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DES3 / References: UniProt: P13726 |
#4: Chemical | ChemComp-N1H / { |
#5: 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: 3.03 Å3/Da / Density % sol: 59.41 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.1 M CITRATE, 16-18% PEG5000 MME, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 27, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 28395 / Num. obs: 28367 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.54→2.65 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DAN Resolution: 2.54→20 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.54→20 Å
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Refine LS restraints |
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