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Yorodumi- PDB-2d1j: Factor Xa in complex with the inhibitor 2-[[4-[(5-chloroindol-2-y... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d1j | ||||||
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Title | Factor Xa in complex with the inhibitor 2-[[4-[(5-chloroindol-2-yl)sulfonyl]piperazin-1-yl] carbonyl]thieno[3,2-b]pyridine n-oxide | ||||||
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: 2.2 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: 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. #2: 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 | 2d1j.cif.gz | 74 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d1j.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 2d1j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d1j_validation.pdf.gz | 466.7 KB | Display | wwPDB validaton report |
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Full document | 2d1j_full_validation.pdf.gz | 468.6 KB | Display | |
Data in XML | 2d1j_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 2d1j_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/2d1j ftp://data.pdbj.org/pub/pdb/validation_reports/d1/2d1j | HTTPS FTP |
-Related structure data
Related structure data | 1wu1C 1faxS 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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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: 5847.532 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-D01 / | #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: 2.59 Å3/Da / Density % sol: 52.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, seeding / pH: 5 Details: pH 5.00, VAPOR DIFFUSION, SEEDING, temperature 293K |
-Data collection
Diffraction | Mean temperature: 300 K | |||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 / Wavelength: 1.5418 Å | |||||||||
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 1, 2000 / Details: monochromator | |||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→33.25 Å / Num. all: 17081 / Num. obs: 17081 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.57 % / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 14.6 | |||||||||
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.62 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1662 / Rsym value: 0.305 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY REFINEMENT Starting model: 1FAX Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.742 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.058 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.277 Å / Total num. of bins used: 15
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