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PDB ID Mentions in PubMed Central Article count: 5

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Small-Molecule Inhibitors of GSK-3: Structural Insights and Their Application to Alzheimer's Disease Models.

(2012) Int J Alzheimers Dis 2012

PubMed: 22888461 | PubMedCentral: PMC3408674 | DOI: 10.1155/2012/381029

The compounds 25 and 26 were docked into the ATP binding site of GSK-3 β (PDB code 1R0E).

Several small-molecule inhibitor/GSK-3 complexes can be extracted from the Protein Data Bank (PDB) (PDB codes: 3PUP (15), 1Q4L (25), 1Q3D (25), 1Q41 (25), 1Q3W (25), 1R0E (34), 2OW3 (40), 2JLD (55), 3M1S (56), 1UV5 (65), 3I4B (113), 3F7Z (119), 3F88 (119), 3GB2 (120), 1Q5K (124), 2O5K (127), 3L1S (130), 3Q3B (136), 1I09 (138)).

PDB code 1R0E [ 40 ].

Publication Year: 2012

Implementation of multiple-instance learning in drug activity prediction.

(2012) BMC Bioinformatics 13 Suppl 15

PubMed: 23046442 | PubMedCentral: PMC3439725 | DOI: 10.1186/1471-2105-13-S15-S3

Table 8 Validations on the prediction of bioactive conformers ID a Name b PDB ID c Contribution d Rank e n i f 23 AR 1Q5K 2.792 3 117 37 Benzoimidazole-1 2O5K 0 N.A. g 138 50 Jonjon-1 2OW3 2.827 6 38 ... 9 LM-4 1Q3W 0.858 1 2 60 LM-5 1UV5 11.941 1 3 77 LM-29 1Q41 8.576 2 7 97 Maleimide 1R0E 0 N.A. g 121 98 OxaD-0 3F7Z 10.629 1 53 99 OxaD-00 3GB2 4.637 2 9 153 Pyzo-11 3L1S 10.371 1 11 198 RM-0 1Q4L 5.568 2 25 199 Staurosporine 1Q3D 22.359 1 5 a Molecule index in the data set; b molecular name in the data set; c Protein Data Bank index for the protein structure from which the experimental conformer was extracted; d contribution f C i j * calculated using equation 6; e the rank in the set of contributions; f the number of conformers for each molecule; g the rank cannot be determined and the conformer was predicted to be irrelevant to classification based on the MILES method.

Publication Year: 2012

From on-target to off-target activity: identification and optimisation of Trypanosoma brucei GSK3 inhibitors and their characterisation as anti-Trypanosoma brucei drug discovery lead molecules.

(2013) ChemMedChem 8

PubMed: 23776181 | PubMedCentral: PMC3728731 | DOI: 10.1002/cmdc.201300072

32 A highly conserved water molecule (H 2 0 82 in 1R0E) was kept in the structure used for docking.

41 Subsequently, Modeller 9.2 42 was used to build homology models of Tb GSK3 short, whereas the human GSK3β crystal structure (PDB code 1R0E) served as template.

The tertiary structure of Lm GSK3 (PDB code 3E3P) is very similar to that of Hs GSK3β (PDB code 1R0E), but several binding pocket residues are missing in the Leishmania crystal structure, as no clearly defined electron density was present.

The Tb GSK3 sequence is 52 % identical and 71 % similar to the sequence in the Hs GSK3β structure (PDB code 1R0E).

Biol 1993 234 779 815 8254673 43 Allard J Nikolcheva T Gong L Wang J Dunten P Avnur Z Waters R Sun Q Skinner B PDB ID: 1R0E, 2004 , 44 Benkert P Tosatto SCE Schomburg D Proteins 2008 71 261 277 17932912 45 Benkert P Kuenzli M Schwede T Nucleic Acids Res 2009 37 W510 W514 19429685 46 Gerber PR Muller K J. Comput.

Figure 1 Superposition of the Hs GSK3β crystal structure (PDB code 1R0E) with the homology model of Tb GSK3.

28 Table 1 Residue differences in the ATP binding sites of Hs GSK3β and Tb GSK3 Kinase pocket region Hs GSK3β [a] Tb GSK3 [b] Hinge region D133 E Y134 F Gatekeeper L132 M E1 Y140 H Q185 H Adenine pocket I62 A Q72 L G-loop N64 Q S66 T [a] PDB code 1R0E.

Publication Year: 2013

Drug activity prediction using multiple-instance learning via joint instance and feature selection.

(2013) BMC Bioinformatics 14 Suppl 14

PubMed: 24267824 | PubMedCentral: PMC3850986 | DOI: 10.1186/1471-2105-14-S14-S16

The selected conformers are clustered into eight groups based on their shape complementarity to the receptor grids (PDB IDs: 1Q3W, 1Q4L, 1R0E, 1UV5, 2OW3, F88, 3GB2, 3ZRM).

Receptor grid preparation We downloaded a set of 20 PDB structural files of GSK-3 β from the RCSB Protein DataBank (PDB) [ 29 ] (PDB IDs: 1H8F, 109U, 1Q3D, 1Q3W, 1Q4L, 1Q5K, 1Q41, 1R0E, 1UV5, 2O5K, 2OW3, 3DU8, 3F7Z, 3F88, 3GB2, 3I4B, 3Q3B, 3ZRK, 3ZRL, and 3ZRM).

Publication Year: 2013

The design and synthesis of potent and selective inhibitors of Trypanosoma brucei glycogen synthase kinase 3 for the treatment of human african trypanosomiasis.

(2014) J Med Chem 57

PubMed: 25198388 | PubMedCentral: PMC4175002 | DOI: 10.1021/jm500239b

As we were mainly interested in aminopyrazoles with less extended R 1 groups, the crystal structure with Phe67 pointing toward the hinge (with structure 1r0e as a representative) was more suited as mo... el system.

A highly conserved water molecule (H 2 O 82 in 1r0e or H 2 O 2134 in 2vu3) was kept in all three protein structures used for docking.

For this analysis, all residues that are located within 6 Å of the ligand bound to the template structure (1r0e) were considered.

Figure 3 Superposition of the binding sites of the homology model of TbGSK3 short (blue carbon atoms) with (A) the HsGSK3β crystal structure (PDB code 1r0e) and (B) the HsCDK2 crystal structure (PDB code 2vu3).

26 Subsequently, Modeler 9.2 27 was used to build homology models of Tb GSK3 short, whereas the Hs GSK3β crystal structure (PDB code 1r0e) served as template.

28 The active sites were defined as the areas within 7 Å of the co-crystallized ligands of Hs CDK2 (PDB code 2vu3) 19 and Hs GSK3β (PDB code 1r0e) 29 or the equivalent residues in the homology model of Tb GSK3.

Publication Year: 2014