+Open data
-Basic information
Entry | Database: PDB / ID: 2vwm | ||||||
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Title | Aminopyrrolidine Factor Xa inhibitor | ||||||
Components |
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Keywords | BLOOD CLOTTING / HYDROLASE / CATION / PLASMA / CALCIUM / ZYMOGEN / PROTEASE / INHIBITOR / POLYMORPHISM / GLYCOPROTEIN / GAMMA-CARBOXYGLUTAMIC ACID / COAGULATION FACTOR / HYDROXYLATION / SERINE PROTEASE / EGF-LIKE DOMAIN / CLEAVAGE ON PAIR OF BASIC RESIDUES | ||||||
Function / homology | Function and homology information coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins ...coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / phospholipid binding / Golgi lumen / blood coagulation / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Groebke-Zbinden, K. / Banner, D.W. / Benz, J.M. / Blasco, F. / Decoret, G. / Himber, J. / Kuhn, B. / Panday, N. / Ricklin, F. / Risch, P. ...Groebke-Zbinden, K. / Banner, D.W. / Benz, J.M. / Blasco, F. / Decoret, G. / Himber, J. / Kuhn, B. / Panday, N. / Ricklin, F. / Risch, P. / Schlatter, D. / Stahl, M. / Unger, R. / Haap, W. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2009 Title: Design of Novel Aminopyrrolidine Factor Xa Inhibitors from a Screening Hit. Authors: Zbinden, K.G. / Anselm, L. / Banner, D.W. / Benz, J.M. / Blasco, F. / Decoret, G. / Himber, J. / Kuhn, B. / Panday, N. / Ricklin, F. / Risch, P. / Schlatter, D. / Stahl, M. / Thomi, S. / Unger, R. / Haap, W. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vwm.cif.gz | 143.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vwm.ent.gz | 111.2 KB | Display | PDB format |
PDBx/mmJSON format | 2vwm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/2vwm ftp://data.pdbj.org/pub/pdb/validation_reports/vw/2vwm | HTTPS FTP |
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-Related structure data
Related structure data | 2vvcSC 2vvuC 2vvvC 2vwlC 2vwnC 2vwoC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 27172.980 Da / Num. of mol.: 2 / Fragment: PEPTIDASE S1 DOMAIN, RESIDUES 235-475 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00742, coagulation factor Xa #2: Protein | Mass: 6060.816 Da / Num. of mol.: 2 / Fragment: EGF2, RESIDUES 126-180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00742, coagulation factor Xa #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Nonpolymer details | HETGROUP LZI : THE CYCLOPROPYL-METHYL GROUP OF THE INHIBITOR HAS NO ELECTRON DENSITY.THE AMIDE ...HETGROUP LZI : THE CYCLOPROPY | Sequence details | ARG-GLU MUTANT.THE RESIDUE NUMBERING IN THE CATALYTIC DOMAIN FOLLOWS THAT OF CHYMOTRYPS | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.3 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 19, 2005 / Details: OSMICS |
Radiation | Monochromator: OSMICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. obs: 36648 / % possible obs: 91.6 % / Observed criterion σ(I): -3 / Redundancy: 4.01 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.96→2.07 Å / Redundancy: 3.93 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 6.57 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VVC Resolution: 1.96→74.74 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.889 / SU B: 5.249 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.214 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→74.74 Å
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Refine LS restraints |
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