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- PDB-1wut: Acyl Ureas as Human Liver Glycogen Phosphorylase Inhibitors for t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1wut | ||||||
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Title | Acyl Ureas as Human Liver Glycogen Phosphorylase Inhibitors for the Treatment of Type 2 Diabetes | ||||||
![]() | Glycogen phosphorylase, muscle form | ||||||
![]() | TRANSFERASE / glycogenolysis / type 2 diabetes | ||||||
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 | ![]() ![]() | ||||||
![]() | Klabunde, T. / Wendt, K.U. / Kadereit, D. / Brachvogel, V. / Burger, H.-J. / Herling, A.W. / Oikonomakos, N.G. / Kosmopoulou, M.N. / Schmoll, D. / Sarubbi, E. ...Klabunde, T. / Wendt, K.U. / Kadereit, D. / Brachvogel, V. / Burger, H.-J. / Herling, A.W. / Oikonomakos, N.G. / Kosmopoulou, M.N. / Schmoll, D. / Sarubbi, E. / von Roedern, E. / Schonafinger, K. / Defossa, E. | ||||||
![]() | ![]() Title: Crystallographic studies on acyl ureas, a new class of glycogen phosphorylase inhibitors, as potential antidiabetic drugs Authors: Oikonomakos, N.G. / Kosmopoulou, M.N. / Chrysina, E.D. / Leonidas, D.D. / Kostas, I.D. / Wendt, K.U. / Klabunde, T. / Defossa, E. #1: ![]() Title: A new allosteric site in glycogen phosphorylase b as a target for drug interactions Authors: Oikonomakos, N.G. / Skamnaki, V.T. / Tsitsanou, K.E. / Gavalas, N.G. / Johnson, L.N. #2: ![]() Title: The structure of glycogen phosphorylase b with an alkyldihydropyridine-dicarboxylic acid compound, a novel and potent inhibitor Authors: Zographos, S.E. / Oikonomakos, N.G. / Tsitsanou, K.E. / Leonidas, D.D. / Chrysina, E.D. / Skamnaki, V.T. / Bischoff, H. / Goldmann, S. / Watson, K.A. / Johnson, L.N. #3: ![]() Title: Human liver glycogen phosphorylase inhibitors bind at a new allosteric site Authors: Rath, V.L. / Ammirati, M. / Danley, D.E. / Ekstrom, J.L. / Gibbs, E.M. / Hynes, T.R. / Mathiowetz, A.M. / McPherson, R.K. / Olson, T.V. / Treadway, J.L. / Hoover, D.J. #4: Journal: Bioorg.Med.Chem.Lett. / Year: 2003 Title: A new class of glycogen phosphorylase inhibitors Authors: Lu, Z. / Bohn, J. / Bergeron, R. / Deng, Q. / Ellsworth, K.P. / Geissler, W.M. / Harris, G. / McCann, P.E. / McKeever, B. / Myers, R.W. / Saperstein, R. / Willoughby, C.A. / Yao, J. / Chapman, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.6 KB | Display | ![]() |
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PDB format | ![]() | 146.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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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Details | Dimeric glycogen phosphorylase is the physiologiacally active species |
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Components
#1: Protein | Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-PLP / |
#3: Chemical | ChemComp-BN2 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 48.91 % |
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Crystal grow | Temperature: 298 K / Method: small tubes / pH: 6.7 Details: 10mM Bes buffer, 3mM DDT, pH 6.7, SMALL TUBES, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 30, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→29.5 Å / Num. all: 394073 / Num. obs: 44163 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.26→2.3 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 5.9 / Num. unique all: 2029 / % possible all: 88.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 29 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.26→29.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.26→2.4 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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