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Open data
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Basic information
Entry | Database: PDB / ID: 7yi7 | ||||||
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Title | Crystal structure of Human HPSE1 in complex with inhibitor | ||||||
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![]() | HYDROLASE/INHIBITOR / Endo-glucoronidase / Heparanase-1 / HEP / HPA / HPA1 / HPR1 / HPSE1 / HSE1 / HYDROLASE / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() heparanase / heparanase activity / regulation of hair follicle development / heparin metabolic process / proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / positive regulation of hair follicle development / HS-GAG degradation / protein transmembrane transport ...heparanase / heparanase activity / regulation of hair follicle development / heparin metabolic process / proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / positive regulation of hair follicle development / HS-GAG degradation / protein transmembrane transport / syndecan binding / vascular wound healing / angiogenesis involved in wound healing / establishment of endothelial barrier / positive regulation of osteoblast proliferation / positive regulation of vascular endothelial growth factor production / positive regulation of blood coagulation / lysosomal lumen / cell-matrix adhesion / : / extracellular matrix / specific granule lumen / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lysosome / membrane raft / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular space / extracellular region / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mima, M. / Fujimoto, N. / Imai, Y. | ||||||
Funding support | 1items
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![]() | ![]() Title: Lead identification of novel tetrahydroimidazo[1,2-a]pyridine-5-carboxylic acid derivative as a potent heparanase-1 inhibitor. Authors: Imai, Y. / Wakasugi, D. / Suzuki, R. / Kato, S. / Sugisaki, M. / Mima, M. / Miyagawa, H. / Endo, M. / Fujimoto, N. / Fukunaga, T. / Kato, S. / Kuroda, S. / Takahashi, T. / Kakinuma, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.1 KB | Display | ![]() |
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PDB format | ![]() | 79.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 795.6 KB | Display | ![]() |
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Full document | ![]() | 799 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 24.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yjcC ![]() 5e8mS 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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Unit cell |
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Components
#1: Protein | Mass: 43464.074 Da / Num. of mol.: 1 / Mutation: K307R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 8273.514 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Chemical | ChemComp-IUV / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4 Details: 12% w/v Polyethylene glycol 3,350, 100 mM Sodium malonate pH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→21.73 Å / Num. obs: 11532 / % possible obs: 99.4 % / Redundancy: 5.1 % / CC1/2: 0.983 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.8→2.95 Å / Num. unique obs: 1661 / CC1/2: 0.722 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5E8M Resolution: 2.8→21.73 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.897 / SU B: 30.68 / SU ML: 0.52 / Cross valid method: THROUGHOUT / ESU R Free: 0.467 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.406 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→21.73 Å
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Refine LS restraints |
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