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Application of consensus scoring and principal component analysis for virtual screening against ?-secretase (BACE-1).
(2012) PLoS One 7
PubMed: 22701601 | PubMedCentral: PMC3372491 | DOI: 10.1371/journal.pone.0038086
Preparation of the Protein Structure The ligand-bound (1W51) structure of BACE-1 was used  .
Individual Performance of Scoring Functions Upon docking 10,000 compounds of the training set with Surflex, every compound yields 30 poses in the active pocket of the target (1W51), and no solution was found on the outside of the active pocket.
g003 Figure 3 Binding modes of compounds in the BACE-1 catalytic site (PDB entry: 1W51).
Publication Year: 2012
Exploring the binding of BACE-1 inhibitors using comparative binding energy analysis (COMBINE).
(2012) BMC Struct Biol 12
PubMed: 22925713 | PubMedCentral: PMC3533579 | DOI: 10.1186/1472-6807-12-21
In comparison to the approach used, e.g., the COMBINE model built from a single X-ray crystal structure (1W51), the method using the actual complexes in the PDB was similar to the flexible docking app... oach, in which the effects of side-chains of several residues were considered.
As depicted in Figure 2 A and B, both the 3-PC model (built from a single X-ray crystal structure) and 5-PC model (built from the actual complexes present in the PDB) behaved well for most of the compounds, However, the 1TQF ligand (inhibitor 2, co-crystallized ligand 32P [ 27 ]) was always determined to be an outlier in the COMBINE analysis, whether or not it was refined before being placed into the binding pocket of 1W51, or built from the actual complexes present in the PDB.
Energy minimization of complexes For comparison purposes, we not only performed the energy minimization on the BACE-1/inhibitor complexes (each inhibitor and the A chain of 1W51) with the above-mentioned protocols, but also applied a similar energy minimization approach on the 46 complexes present in the PDB.
Followed by energy minimization, for comparison purposes, we not only performed COMBINE analysis on the BACE-1/inhibitor complexes (each inhibitor and the A chain of 1W51), but also performed COMBINE analysis on the actual complexes present in the PDB after a similar energy refinement.
The 46 co-crystallized ligands were aligned in the binding pocket of 1W51 by the superimposition method using the C α atoms (1W51 structure as the reference).
From the comparative analysis of the BACE-1 X-ray structures, it is clear that the 10S loop, a short loop located at the base of the S 3 sp, displays two primary low-energy conformations: an open conformation (e.g., 1W51, 1TQF, 2F3E and 2B8V) and a closed conformation (e.g., 1FKN, 1M4H and 1XS7).
The 46 X-ray structures of BACE-1/inhibitor complexes used in this study are 1W51, 1TQF, 1YM2, 1YM4, 2B8V, 2F3E, 2F3F, 2IQG, 2IRZ, 2IS0, 2OAH, 2OHL, 2OHM, 2OHP, 2OHQ, I2OHR, 2OHS, 2OHT, 2OHU, 2P83, 2PH6, 2B8L, 2QZL, 2ZE1, 2QP8, 2VIE, 2VJ7, 2VJ9, 2VNM, 2VNN, 2WF0, 2WF1, 2ZDZ, 2FDP, 3CIB, 3CIC, 3CID, 3DUY, 3DV1, 2P4J, 3FKT, 2QK5, 1XS7, 1FKN and 1M4H.
Cartoon representation of the active site of the four BACE-1 X-ray structures used for the superposition study (1W51, 1FKN, 2OHL, and 2OHS are in green, cyan, magenta and yellow, respectively) with compound 1 shown as ball and sticks; hydrogen atoms are omitted for reasons of clarity.
Fragment-based Binding Efficiency Indices in Bioactive Molecular Design: A Computational Approach to BACE-1 Inhibitors.
(2013) Iran J Pharm Res 12
PubMed: 24250649 | PubMedCentral: PMC3813291 | DOI: null
Table 4 Experimental IC 50 s for crystallographic BACE-1 inhibitors and structure-based binding indices in related fragments PDB code IC 50 s of BACE1 inhibitors (nM) Docked fragments BE LE BEI 1W51 5... 0 -10.55 0.377 20.67 2P83 11 -10.96 0.391 21.47 3L58 15-80 -11.84 0.377 23.20 Priority order 2P83>3L58>1W51 3L58>2P83>1W51 2P83>1W51≈3L58 3L58>2P83>1W51 Experimental data showed that the priority order was not retained in docked fragments due to the absence of side chains.
Publication Year: 2013
Coffee and caffeine potentiate the antiamyloidogenic activity of melatonin via inhibition of A? oligomerization and modulation of the Tau-mediated pathway in N2a/APP cells.
(2015) Drug Des Devel Ther 9
PubMed: 25565776 | PubMedCentral: PMC4284031 | DOI: 10.2147/DDDT.S71106
Materials and methods Molecular docking We employed the Discovery Studio program 3.1 designed by Accelrys Inc. (San Diego, CA, USA) to dock Caff and Mel into the active sites of ten human BACE1 struct... res (protein data bank [PDB] identification codes: 1FKN, 2OHU, 1W51, 2P4J, 2VKM, 4DH6, 3DV5, 2QU3, 3U6A, and 4FRS) as previously described by us.
Publication Year: 2015
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