+Open data
-Basic information
Entry | Database: PDB / ID: 7yjc | ||||||
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Title | Crystal structure of Human HPSE1 in complex with inhibitor | ||||||
Components |
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Keywords | HYDROLASE/INHIBITOR / Endo-glucoronidase / Heparanase-1 / HEP / HPA / HPA1 / HPR1 / HPSE1 / HSE1 / HYDROLASE / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information heparanase / heparanase activity / regulation of hair follicle development / heparan sulfate proteoglycan catabolic process / heparin metabolic process / proteoglycan metabolic process / HS-GAG degradation / positive regulation of hair follicle development / beta-glucuronidase activity / syndecan binding ...heparanase / heparanase activity / regulation of hair follicle development / heparan sulfate proteoglycan catabolic process / heparin metabolic process / proteoglycan metabolic process / HS-GAG degradation / positive regulation of hair follicle development / beta-glucuronidase activity / syndecan binding / protein transmembrane transport / 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 / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / membrane raft / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular space / extracellular region / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Mima, M. / Fujimoto, N. / Imai, Y. | ||||||
Funding support | 1items
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Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yjc.cif.gz | 107.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yjc.ent.gz | 78.7 KB | Display | PDB format |
PDBx/mmJSON format | 7yjc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yjc_validation.pdf.gz | 857.9 KB | Display | wwPDB validaton report |
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Full document | 7yjc_full_validation.pdf.gz | 867.7 KB | Display | |
Data in XML | 7yjc_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 7yjc_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/7yjc ftp://data.pdbj.org/pub/pdb/validation_reports/yj/7yjc | HTTPS FTP |
-Related structure data
Related structure data | 7yi7C 5e8mS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Plasmid: pIEx4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y251, heparanase |
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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.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Plasmid: pIEx4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y251, heparanase |
#3: Chemical | ChemComp-IVO / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.3 Details: 20% w/v Polyethylene glycol 3,350, 200 mM Ammonium chloride; pH 6.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→77.95 Å / Num. obs: 21509 / % possible obs: 98.7 % / Redundancy: 5.6 % / CC1/2: 0.993 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.3→2.42 Å / Num. unique obs: 3121 / CC1/2: 0.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5E8M Resolution: 2.3→77.95 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.82 / SU B: 16.648 / SU ML: 0.393 / Cross valid method: THROUGHOUT / ESU R: 0.513 / ESU R Free: 0.338 / 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: 42.901 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→77.95 Å
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