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Yorodumi- PDB-2y7z: Structure and property based design of factor Xa inhibitors: pyrr... -
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-Basic information
Entry | Database: PDB / ID: 2y7z | ||||||
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Title | Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with aminoindane and phenylpyrrolidine P4 motifs | ||||||
Components |
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Keywords | BLOOD CLOTTING / HYDROLASE / SERINE PROTEASE / BLOOD COAGULATION | ||||||
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 / SYNCHROTRON / OTHER / Resolution: 1.84 Å | ||||||
Authors | Young, R.J. / Adams, C. / Blows, M. / Brown, D. / Burns-Kurtis, C.L. / Chaudry, L. / Chan, C. / Convery, M.A. / Davies, D.E. / Exall, A.M. ...Young, R.J. / Adams, C. / Blows, M. / Brown, D. / Burns-Kurtis, C.L. / Chaudry, L. / Chan, C. / Convery, M.A. / Davies, D.E. / Exall, A.M. / Foster, G. / Harling, J.D. / Hortense, E. / Irving, W.R. / Irvine, S. / Jackson, S. / Kleanthous, S. / Pateman, A.J. / Patikis, A.N. / Roethka, T.J. / Senger, S. / Stelman, G.J. / Toomey, J.R. / West, R.I. / Whittaker, C. / Zhou, P. / Watson, N.S. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2011 Title: Structure and Property Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Aminoindane and Phenylpyrrolidine P4 Motifs. Authors: Young, R.J. / Adams, C. / Blows, M. / Brown, D. / Burns-Kurtis, C.L. / Chan, C. / Chaudry, L. / Convery, M.A. / Davies, D.E. / Exall, A.M. / Foster, G. / Harling, J.D. / Hortense, E. / ...Authors: Young, R.J. / Adams, C. / Blows, M. / Brown, D. / Burns-Kurtis, C.L. / Chan, C. / Chaudry, L. / Convery, M.A. / Davies, D.E. / Exall, A.M. / Foster, G. / Harling, J.D. / Hortense, E. / Irvine, S. / Irving, W.R. / Jackson, S. / Kleanthous, S. / Pateman, A.J. / Patikis, A.N. / Roethka, T.J. / Senger, S. / Stelman, G.J. / Toomey, J.R. / West, R.I. / Whittaker, C. / Zhou, P. / Watson, N.S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" 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 | 2y7z.cif.gz | 76.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y7z.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 2y7z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y7z_validation.pdf.gz | 755.4 KB | Display | wwPDB validaton report |
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Full document | 2y7z_full_validation.pdf.gz | 756.3 KB | Display | |
Data in XML | 2y7z_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 2y7z_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/2y7z ftp://data.pdbj.org/pub/pdb/validation_reports/y7/2y7z | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 28550.596 Da / Num. of mol.: 1 / 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 |
-Non-polymers , 4 types, 211 molecules
#3: Chemical | ChemComp-C0Z / |
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#4: Chemical | ChemComp-CA / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Details
Sequence details | SEQUENCE DATABASE RESIDUES 1-45 (THE GLA DOMAIN) WERE BIOCHEMICA |
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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: 1.84 Å3/Da / Density % sol: 33.06 % / Description: NONE |
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Crystal grow | Method: vapor diffusion / pH: 5.75 Details: CRYSTALLISATION WAS CARRIED OUT USING VAPOUR DIFFUSION IN 2UL DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN AND WELL SOLUTION. WELL SOLUTION CONTAINED 16-20% PEG6K, 50MM MES-NAOH (PH 5.5-6), 5MM CACL2 AND 50MM NACL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 19, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→25 Å / Num. obs: 23894 / % possible obs: 83.9 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 26.138 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.84→1.88 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.76 / % possible all: 88.4 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.84→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.092 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME RESIDUES IN CHAINS A AND B ARE NOT OBSERVED IN THE ELECTRON DENSITY.
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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: 30.384 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→20 Å
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Refine LS restraints |
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