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Yorodumi- PDB-1qbn: Bovine Trypsin 2-[amino(imino)methyl]-2-hydroxyphenoxy]-6-[3-(4,5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qbn | ||||||
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Title | Bovine Trypsin 2-[amino(imino)methyl]-2-hydroxyphenoxy]-6-[3-(4,5-dihydro-1H-imidazol-2-yl)phenoxy]pyridine-4-carboxylic Acid (ZK-806688) Complex | ||||||
Components | PROTEIN (TRYPSIN) | ||||||
Keywords | HYDROLASE / SERINE PROTEINASE / PROTEIN-INHIBITOR COMPLEX / S1 POCKET | ||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / DIRECT REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Whitlow, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystallographic analysis of potent and selective factor Xa inhibitors complexed to bovine trypsin. Authors: Whitlow, M. / Arnaiz, D.O. / Buckman, B.O. / Davey, D.D. / Griedel, B. / Guilford, W.J. / Koovakkat, S.K. / Liang, A. / Mohan, R. / Phillips, G.B. / Seto, M. / Shaw, K.J. / Xu, W. / Zhao, Z. ...Authors: Whitlow, M. / Arnaiz, D.O. / Buckman, B.O. / Davey, D.D. / Griedel, B. / Guilford, W.J. / Koovakkat, S.K. / Liang, A. / Mohan, R. / Phillips, G.B. / Seto, M. / Shaw, K.J. / Xu, W. / Zhao, Z. / Light, D.R. / Morrissey, M.M. #1: Journal: FEBS Lett. / Year: 1978 Title: Crystal Structure Analysis and Refinement of Two Variants of Trigonal Trypsinogen Authors: Bode, W. / Huber, R. #2: Journal: J.Med.Chem. / Year: 1999 Title: Design, Synthesis, and Activity of 2,6-Diphenoxypyridine-Derived Factor Xa Inhibitors Authors: Phillips, G. / Davey, D. / Eagen, K. / Ng, H.P. / Pinkerton, M. / Koovakkat, S.K. / Whitlow, M. / Liang, A. / Trinh, L. / Morrissey, M.M. #3: Journal: J.Med.Chem. / Year: 1998 Title: Discovery of N-[2-[5-[Amino(imino)methyl]-2-hydroxyphenoxy]-3,5-difluoro-6-[3-(4,5-dihydro-1-methyl-1H-imidazol-2-yl)phenoxy] pyridin-4-yl-N-methylglycine (ZK-807834): A Potent, Selective and ...Title: Discovery of N-[2-[5-[Amino(imino)methyl]-2-hydroxyphenoxy]-3,5-difluoro-6-[3-(4,5-dihydro-1-methyl-1H-imidazol-2-yl)phenoxy] pyridin-4-yl-N-methylglycine (ZK-807834): A Potent, Selective and Orally Active Inhibitor of the Blood Coagulation Enzyme Factor Xa Authors: Phillips, G.B. / Buckman, B.O. / Davey, D.D. / Eagen, K.A. / Guilford, W.J. / Hinchman, J. / Ho, E. / Koovakkat, S. / Liang, A. / Light, D.R. / Mohan, R. / Ng, H.P. / Post, J. / Smith, D. / ...Authors: Phillips, G.B. / Buckman, B.O. / Davey, D.D. / Eagen, K.A. / Guilford, W.J. / Hinchman, J. / Ho, E. / Koovakkat, S. / Liang, A. / Light, D.R. / Mohan, R. / Ng, H.P. / Post, J. / Smith, D. / Subramanyam, B. / Sullivan, M.E. / Trinh, L. / Vergona, R. / Walters, J. / White, K. / Whitlow, M. / Wu, S. / Xu, W. / Morrissey, M.M. #4: Journal: FEBS Lett. / Year: 1995 Title: Crystal structures of factor Xa specific inhibitors in complex with trypsin: structural grounds for inhibition of factor Xa and selectivity against thrombin Authors: Stubbs, M.T. / Huber, R. / Bode, W. #5: Journal: Methods (San Diego) / Year: 1990 Title: Analytical and Production Seeding Techniques Authors: Stura, E.A. / Wilson, I.A. #6: Journal: J.Biol.Chem. / Year: 1996 Title: X-ray structure of Active Site-inhibited Clotting Factor Xa Authors: Brandstetter, H. / Kuhne, A. / Bode, W. / Huber, R. / von der Saal, W. / Wirthensohn, K. / Engh, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qbn.cif.gz | 56.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qbn.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 1qbn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/1qbn ftp://data.pdbj.org/pub/pdb/validation_reports/qb/1qbn | HTTPS FTP |
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-Related 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 a monomer. |
-Components
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Fragment: BOVINE TRYPSIN / Source method: isolated from a natural source / Details: BOEHRINGER MANNHEIM CATALOG NUMBER 109,827 / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00760, trypsin | ||||
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#2: Chemical | #3: Chemical | ChemComp-688 / | #4: 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: 2.05 Å3/Da / Density % sol: 39.82 % Description: STARTING FROM THE TRYPSIN 2-AMINOBENZIMIDAZOLE STRUCTURE | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: MICROCRYSTALS GROWN USING THE HANGING DROP METHOD IN LINBRO CULTURE PLATES. CRYSTALLIZATION RESERVOIRS CONTAIN 1.8 - 2.0 M AMMONIUM SULFATE, 50 MM TRIS HCL, 10 MM CACL2, PH 7.4. SIX UL OF 15 ...Details: MICROCRYSTALS GROWN USING THE HANGING DROP METHOD IN LINBRO CULTURE PLATES. CRYSTALLIZATION RESERVOIRS CONTAIN 1.8 - 2.0 M AMMONIUM SULFATE, 50 MM TRIS HCL, 10 MM CACL2, PH 7.4. SIX UL OF 15 MG/ML BOVINE TRYPSIN IN 20 MM 2-AMINOBENZIMIDAZOLE WAS ADDED TO 6 UL OF RESERVOIR. MACROSEEDING WAS USED TO GROW LARGE CRYSTALS (REF 5). SINGLE CRYSTALS WERE WASHED IN 0.8 M AMMONIUM SULFATE, 50 MM TRIS HCL, 10 MM CACL2, PH 7.4. THE WASHED CRYSTALS WERE PLACED IN A 18 HOUR OLD HANGING, VAPOR DIFFUSION, HANGING DROP, temperature 297K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 15, 1994 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→10 Å / Num. all: 16885 / Num. obs: 16575 / % possible obs: 95.2 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rsym value: 0.075 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.36 / Rsym value: 0.226 / % possible all: 90 |
Reflection | *PLUS Rmerge(I) obs: 0.075 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 90 % / Rmerge(I) obs: 0.226 |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT REPLACEMENT / Resolution: 1.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 Stereochemistry target values: Hendrickson, W.A. (1985): Methods in Enzymology 115, pp. 252-270
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROFFT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 4 % / Rfactor obs: 0.154 / Rfactor Rwork: 0.155 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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