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Yorodumi- PDB-1wu1: Factor Xa in complex with the inhibitor 4-[(5-chloroindol-2-yl)su... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wu1 | ||||||
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Title | Factor Xa in complex with the inhibitor 4-[(5-chloroindol-2-yl)sulfonyl]-2-(2-methylpropyl)-1-[[5-(pyridin-4-yl) pyrimidin-2-yl]carbonyl]piperazine | ||||||
Components |
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Keywords | HYDROLASE / glycoprotein / serine protease / plasma / blood coagulation factor / protein inhibitor complex / calcium-binding | ||||||
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 / RIGID BODY REFINEMENT / Resolution: 2.3 Å | ||||||
Authors | Suzuki, M. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2005 Title: Design, synthesis, and biological activity of non-basic compounds as factor Xa inhibitors: SAR study of S1 and aryl binding sites Authors: Komoriya, S. / Haginoya, N. / Kobayashi, S. / Nagata, T. / Mochizuki, A. / Suzuki, M. / Yoshino, T. / Horino, H. / Nagahara, T. / Suzuki, M. / Isobe, Y. / Furugoori, T. #1: Journal: Proc.Natl.Acad.Sci.Usa / Year: 1998 Title: Structural basis for chemical inhibition of human blood coagulation factor Xa Authors: Kamata, K. / Kawamoto, H. / Honma, T. / Iwama, T. / Kim, S.H. #2: Journal: J.Biol.Chem. / Year: 1996 Title: X-ray structure of active site-inhibited clotting factor Xa. Implications for drug design and substrate recognition Authors: Brandstetter, H. / Kuhne, A. / Bode, W. / Huber, R. / von der Saal, W. / Wirthensohn, K. / Engh, R.A. #3: Journal: J.Mol.Biol. / Year: 1993 Title: Structure of human des(1-45) factor Xa at 2.2 A resolution Authors: Padmanabhan, K. / Padmanabhan, K.P. / Tulinsky, A. / Park, C.H. / Bode, W. / Huber, R. / Blankenship, D.T. / Cardin, A.D. / Kisiel, W. #4: Journal: J.Med.Chem. / Year: 2004 Title: Synthesis and Conformational Analysis of a Non-Amidine Factor Xa Inhibitor That Incorporates 5-Methyl-4,5,6,7-tetrahydrothiazolo[5,4-c]pyridine as S4 Binding Element Authors: Haginoya, N. / Kobayashi, S. / Komoriya, S. / Yoshino, T. / Suzuki, M. / Shimada, T. / Watanabe, K. / Hirokawa, Y. / Furugori, T. / Nagahara, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wu1.cif.gz | 75.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wu1.ent.gz | 53.3 KB | Display | PDB format |
PDBx/mmJSON format | 1wu1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/1wu1 ftp://data.pdbj.org/pub/pdb/validation_reports/wu/1wu1 | HTTPS FTP |
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-Related structure data
Related structure data | 2d1jC 1faxS 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: 26346.000 Da / Num. of mol.: 1 / Fragment: RESIDUES 16-243 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa | ||||
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#2: Protein | Mass: 10386.538 Da / Num. of mol.: 1 / Fragment: RESIDUES 85-138 / Source method: isolated from a natural source / Details: PROTEOLYTIC CLEAVAGE PRODUCT / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa | ||||
#3: Chemical | #4: Chemical | ChemComp-D91 / | #5: 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: 2.2 Å3/Da / Density % sol: 44.21 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG6000, NaAcetate, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 / Wavelength: 1.542 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 13, 1999 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→39.51 Å / Num. obs: 13656 / % possible obs: 90.6 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.064 / Rsym value: 0.338 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.89 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.89 / Rsym value: 0.338 / % possible all: 84.3 |
Reflection | *PLUS Highest resolution: 2.3 Å / Observed criterion σ(I): 0 / Redundancy: 2.9 % |
Reflection shell | *PLUS % possible obs: 84.3 % / Mean I/σ(I) obs: 2.89 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY REFINEMENT Starting model: 1FAX Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.604 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.338 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Total num. of bins used: 15
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 25 Å / Rfactor Rwork: 0.191 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 45.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.38 Å |