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Yorodumi- PDB-8est: REACTION OF PORCINE PANCREATIC ELASTASE WITH 7-SUBSTITUTED 3-ALKO... -
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-Basic information
Entry | Database: PDB / ID: 8est | ||||||
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Title | REACTION OF PORCINE PANCREATIC ELASTASE WITH 7-SUBSTITUTED 3-ALKOXY-4-CHLOROISOCOUMARINS: DESIGN OF POTENT INHIBITORS USING THE CRYSTAL STRUCTURE OF THE COMPLEX FORMED WITH 4-CHLORO-3-ETHOXY-7-GUANIDINO-ISOCOUMARIN | ||||||
Components | PORCINE PANCREATIC ELASTASE | ||||||
Keywords | HYDROLASE(SERINE PROTEINASE) | ||||||
Function / homology | Function and homology information pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.78 Å | ||||||
Authors | Radhakrishnan, R. / Powers, J.C. / Meyerjunior, E.F. | ||||||
Citation | Journal: Biochemistry / Year: 1990 Title: Reaction of porcine pancreatic elastase with 7-substituted 3-alkoxy-4-chloroisocoumarins: design of potent inhibitors using the crystal structure of the complex formed with 4-chloro-3-ethoxy-7- ...Title: Reaction of porcine pancreatic elastase with 7-substituted 3-alkoxy-4-chloroisocoumarins: design of potent inhibitors using the crystal structure of the complex formed with 4-chloro-3-ethoxy-7-guanidinoisocoumarin. Authors: Powers, J.C. / Oleksyszyn, J. / Narasimhan, S.L. / Kam, C.M. #1: Journal: J.Med.Chem. / Year: 1992 Title: Effect of the 7-Amino Substituent on the Inhibitory Potency of Mechanism-Based Isocoumarin Inhibitors for Porcine Pancreatic and Human Neutrophil Elastases: A 1.85-Angstroms X-Ray Structure of ...Title: Effect of the 7-Amino Substituent on the Inhibitory Potency of Mechanism-Based Isocoumarin Inhibitors for Porcine Pancreatic and Human Neutrophil Elastases: A 1.85-Angstroms X-Ray Structure of the Complex between Porcine Pancreatic Elastase and 7-[(N-Tosylphenylalanyl)Amino]-4-Chloro-3-Methoxyisocoumarin Authors: Hernandez, M.A. / Powers, J.C. / Glinski, J. / Oleksyszyn, J. / Vijayalakshmi, J. / Meyerjunior, E.F. #2: Journal: Biochemistry / Year: 1991 Title: Structural Study of Porcine Pancreatic Elastase Complexed with 7-Amino-3-(2-Bromoethoxy)-4-Chloroisocoumarin as a Nonreactivatable Doubly Covalent Enzyme-Inhibitor Complex Authors: Vijayalakshmi, J. / Meyerjunior, E.F. / Kam, C.-M. / Powers, J.C. #3: Journal: J.Am.Chem.Soc. / Year: 1990 Title: The 2.2-Angstrom Resolution X-Ray Crystal Structure of the Complex of Trypsin Inhibited by 4-Chloro-3-Ethoxy-7-Guanidinoisocoumarin: A Proposed Model of the Thrombin-Inhibitor Complex Authors: Chow, M.M. / Meyerjunior, E.F. / Bode, W. / Kam, C.-M. / Radhakrishnan, R. / Vijayalakshmi, J. / Powers, J.C. #4: Journal: Biochemistry / Year: 1989 Title: Human Leukocyte and Porcine Pancreatic Elastase: X-Ray Crystal Structures, Mechanism, Substrate Specificity, and Mechanism-Based Inhibitors Authors: Bode, W. / Meyerjunior, E.F. / Powers, J.C. #5: Journal: J.Mol.Biol. / Year: 1987 Title: Crystal Structures of the Complex of Porcine Pancreatic Elastase with Two Valine-Derived Benzoxazinone Inhibitors Authors: Radhakrishnan, R. / Presta, L.G. / Meyerjunior, E.F. / Wildonger, R. #6: Journal: J.Am.Chem.Soc. / Year: 1985 Title: Stereospecific Reaction of 3-Methoxy-4-Chloro-7-Amino-Isocoumarin with Crystalline Porcine Pancreatic Elastase Authors: Meyerjunior, E.F. / Presta, L.G. / Radhakrishnan, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 8est.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8est.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 8est.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/8est ftp://data.pdbj.org/pub/pdb/validation_reports/es/8est | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: THE FOLLOWING ATOMS WERE TREATED AS DUMMY ATOMS, WHICH MEANS THAT THEY CONTRIBUTED TO THE ENERGY REFINEMENT PART OF EREF BUT NOT TO THE CALCULATED STRUCTURE FACTORS -SER 36C OG, SER 37 OG, ARG 61 ...1: THE FOLLOWING ATOMS WERE TREATED AS DUMMY ATOMS, WHICH MEANS THAT THEY CONTRIBUTED TO THE ENERGY REFINEMENT PART OF EREF BUT NOT TO THE CALCULATED STRUCTURE FACTORS -SER 36C OG, SER 37 OG, ARG 61 (CZ,NH1,NH2), GLN 110 (CG,CD,OE1,NE2), ARG 125 (CG,CD,NE,CZ,NH1,NH2), SO4 247 (O1,O3). |
-Components
#1: Protein | Mass: 25928.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-GIS / |
#5: Water | ChemComp-HOH / |
Compound details | THIS COMPLEX IS ONE OF THE BEST IRREVERSIBLE INHIBITORS THUS FAR REPORTED FOR PPE (KOBS/[I] = ...THIS COMPLEX IS ONE OF THE BEST IRREVERSIB |
Nonpolymer details | THE TITLE INHIBITOR HAS BEEN STUDIED IN TWO RELATED ENZYMES PPE AND BOVINE TRYPSIN (REFERENCE 3). ...THE TITLE INHIBITOR HAS BEEN STUDIED IN TWO RELATED ENZYMES PPE AND BOVINE TRYPSIN (REFERENCE 3). IN THE LATTER CASE, AS WOULD BE EXPECTED, THE POSITIVELY |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.49 % |
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Crystal grow | *PLUS Method: unknown |
-Processing
Software | Name: EREF / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.78→7 Å / Rfactor Rwork: 0.17 Details: THE FOLLOWING ATOMS WERE TREATED AS DUMMY ATOMS, WHICH MEANS THAT THEY CONTRIBUTED TO THE ENERGY REFINEMENT PART OF EREF BUT NOT TO THE CALCULATED STRUCTURE FACTORS -SER 36C OG, SER 37 OG, ...Details: THE FOLLOWING ATOMS WERE TREATED AS DUMMY ATOMS, WHICH MEANS THAT THEY CONTRIBUTED TO THE ENERGY REFINEMENT PART OF EREF BUT NOT TO THE CALCULATED STRUCTURE FACTORS -SER 36C OG, SER 37 OG, ARG 61 (CZ,NH1,NH2), GLN 110 (CG,CD,OE1,NE2), ARG 125 (CG,CD,NE,CZ,NH1,NH2), SO4 247 (O1,O3). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→7 Å
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