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- PDB-4cto: Glucopyranosylidene-spiro-iminothiazolidinone, a New Bicyclic Rin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cto | ||||||
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Title | Glucopyranosylidene-spiro-iminothiazolidinone, a New Bicyclic Ring System: Synthesis, Derivatization, and Evaluation as Glycogen Phosphorylase Inhibitors by Enzyme Kinetic and Crystallographic Methods | ||||||
![]() | GLYCOGEN PHOSPHORYLASE, MUSCLE FORM | ||||||
![]() | TRANSFERASE / TYPE 2 DIABETES / INHIBITOR / STRUCTURE-BASED DRUG DESIGN | ||||||
Function / homology | ![]() glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Alexacou, K.M. / Papakonstantinou, M. / Leonidas, D.D. / Zographos, S.E. / Chrysina, E.D. | ||||||
![]() | ![]() Title: Glucopyranosylidene-Spiro-Iminothiazolidinone, a New Bicyclic Ring System: Synthesis, Derivatization, and Evaluation for Inhibition of Glycogen Phosphorylase by Enzyme Kinetic and Crystallographic Methods. Authors: Czifrak, K. / Deak, S. / Pahi, A. / Kover, K.E. / Docsa, T. / Gergely, P. / Alexacou, K.M. / Papakonstantinou, M. / Leonidas, D.D. / Zographos, S.E. / Chrysina, E.D. / Somsak, L. #1: ![]() Title: The Structure of a Glycogen Phosphorylase Glucopyranose Spirohydantoin Complex at 1.8 A Resolution and 100 K: The Role of the Water Structure and its Contribution to Binding. Authors: Gregoriou, M. / Noble, M.E. / Watson, K.A. / Garman, E.F. / Krulle, T.M. / De La Fuente, C. / Fleet, G.W. / Oikonomakos, N.G. / Johnson, L.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182 KB | Display | ![]() |
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PDB format | ![]() | 142.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 734.9 KB | Display | ![]() |
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Full document | ![]() | 738.4 KB | Display | |
Data in XML | ![]() | 30.8 KB | Display | |
Data in CIF | ![]() | 44.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ctmC ![]() 4ctnC ![]() 2pydS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 97422.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-M7C / |
#3: Chemical | ChemComp-PLP / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.74 % / Description: NONE |
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Crystal grow | Temperature: 289 K / pH: 6.8 Details: 25MG/ML ENZYME, 1MM SPERMINE, 10MM BES, 3MM DTT, 0.1MM EDTA, PH 6.7, AT 16 DEGREES C. |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 16, 2007 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97976 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→35.7 Å / Num. obs: 74351 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.2 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2PYD Resolution: 1.9→35.5 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.82 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.117 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.009 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→35.5 Å
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Refine LS restraints |
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