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Yorodumi- PDB-2uwl: Selective and Dual Action Orally Active Inhibitors of Thrombin an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uwl | ||||||
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Title | Selective and Dual Action Orally Active Inhibitors of Thrombin and Factor Xa | ||||||
Components | (COAGULATION FACTOR XFactor X) x 2 | ||||||
Keywords | HYDROLASE / TARGET HOPPING / SERINE PROTEASE / EGF-LIKE DOMAIN / POLYMORPHISM / GLYCOPROTEIN / HYDROXYLATION / CALCIUM / ZYMOGEN / COMPLEX / PROTEASE / BLOOD COAGULATION / GAMMA- CARBOXYGLUTAMIC ACID / 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 leukocyte chemotaxis / 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 ...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 leukocyte chemotaxis / 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 / external side of plasma membrane / endoplasmic reticulum lumen / 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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Young, R.J. / Brown, D. / Burns-Kurtis, C.L. / Chan, C. / Convery, M.A. / Hubbard, J.A. / Kelly, H.A. / Pateman, A.J. / Patikis, A. / Senger, S. ...Young, R.J. / Brown, D. / Burns-Kurtis, C.L. / Chan, C. / Convery, M.A. / Hubbard, J.A. / Kelly, H.A. / Pateman, A.J. / Patikis, A. / Senger, S. / Shah, G.P. / Toomey, J.R. / Watson, N.S. / Zhou, P. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2007 Title: Selective and Dual Action Orally Active Inhibitors of Thrombin and Factor Xa. Authors: Young, R.J. / Brown, D. / Burns-Kurtis, C.L. / Chan, C. / Convery, M.A. / Hubbard, J.A. / Kelly, H.A. / Pateman, A.J. / Patikis, A. / Senger, S. / Shah, G.P. / Toomey, J.R. / Watson, N.S. / Zhou, P. | ||||||
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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uwl.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uwl.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 2uwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/2uwl ftp://data.pdbj.org/pub/pdb/validation_reports/uw/2uwl | HTTPS FTP |
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-Related structure data
Related structure data | 2uwoC 2uwpC 1ezqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28550.596 Da / Num. of mol.: 1 / Fragment: ACTIVATED DESGLA, RESIDUES 235-488 / Source method: isolated from a natural source Details: PURCHASED FROM ENZYME RESEARCH LABS. ISOLATED FROM HUMAN BLOOD Source: (natural) HOMO SAPIENS (human) / References: UniProt: P00742, coagulation factor Xa |
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#2: Protein | Mass: 15210.793 Da / Num. of mol.: 1 / Fragment: ACTIVATED DESGLA, RESIDUES 46-179 / Source method: isolated from a natural source Details: PURCHASED FROM ENZYME RESEARCH LABS. ISOLATED FROM HUMAN BLOOD Source: (natural) HOMO SAPIENS (human) / References: UniProt: P00742, coagulation factor Xa |
#3: Chemical | ChemComp-895 / |
#4: Water | ChemComp-HOH / |
Sequence details | SOME RESIDUES IN CHAIN ARE NOT SEEN IN THE ELECTRON DENSITY. SEQUENCE DATABASE RESIDUES 1-45 (THE ...SOME RESIDUES IN CHAIN ARE NOT SEEN IN THE ELECTRON DENSITY. SEQUENCE DATABASE RESIDUES 1-45 (THE GLA DOMAIN) WERE BIOCHEMICA |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 33.63 % |
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Crystal grow | pH: 5.75 Details: 18% PEG6K, 50MM HEPES PH5.75, 10MM CACL2, 150MM NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 20, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 26374 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.97 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.8 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1EZQ Resolution: 1.9→19.96 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.402 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.144 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.66 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.96 Å
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