+Open data
-Basic information
Entry | Database: PDB / ID: 2flb | ||||||
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Title | Discovery of a Novel Hydroxy Pyrazole Based Factor IXa Inhibitor | ||||||
Components |
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Keywords | HYDROLASE/BLOOD CLOTTING / active site-directed / short hydrogen bond-mediated / pyrazole-based 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 / positive regulation of leukocyte chemotaxis / NGF-stimulated transcription / response to cholesterol / response to growth hormone / cytokine receptor activity / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / 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 / circadian rhythm / protein processing / phospholipid binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / cytokine-mediated signaling pathway / Golgi lumen / response to estrogen / positive regulation of angiogenesis / blood coagulation / response to estradiol / protease binding / collagen-containing extracellular matrix / 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 / FOURIER SYNTHESIS / Resolution: 1.95 Å | ||||||
Authors | Katz, B.A. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2006 Title: Discovery of novel hydroxy pyrazole based factor IXa inhibitor. Authors: Vijaykumar, D. / Sprengeler, P.A. / Shaghafi, M. / Spencer, J.R. / Katz, B.A. / Yu, C. / Rai, R. / Young, W.B. / Schultz, B. / Janc, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2flb.cif.gz | 120.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2flb.ent.gz | 94.7 KB | Display | PDB format |
PDBx/mmJSON format | 2flb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/2flb ftp://data.pdbj.org/pub/pdb/validation_reports/fl/2flb | HTTPS FTP |
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-Related structure data
Related structure data | |
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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 assembly is one molecule of factor VIIa (light chain plus heavy chain), one molecule of tissue factor, and one inhibitor molecule (2-(4-Hydroxy-5-phenyl-1H-pyrazol-3-yl)-1H-benzoimidazole-5-carboxamidine |
-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 / Production host: Escherichia coli (E. coli) / References: UniProt: P08709 |
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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 / Production host: Escherichia coli (E. coli) / References: UniProt: P08709 |
#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-6NH / |
#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: 3.05 Å3/Da / Density % sol: 59.67 % |
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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 290.0K |
-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 315 / Detector: CCD / Date: Jun 21, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. all: 57297 / Num. obs: 57297 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.95→2.04 Å / % possible all: 81.34 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.95→7 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.95→7 Å
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Refine LS restraints |
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