Primary Citation PubMed: 16263281
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Molecular shape and medicinal chemistry: a perspective.
(2010) J Med Chem 53
PubMed: 20158188 | PubMedCentral: PMC2874267 | DOI: 10.1021/jm900818s
For instance, if you used the hydroxyethylamine ligand from the PDB code 2B8L ( 32 ) as a probe for virtual screening (which interacts directly with both catalytic aspartic acids Asp 32 and Asp 228 an... occupies regions P1, P2, P3, and P1′), it would be nearly impossible to identify in the top rankings a spiropiperidine (PDB code 3FKT ( 33 )) which interacts with the catalytic aspartic acids via a water molecule and does not occupy regions P2 or P3 at all.
Figure 4 (a) Highest ranked ROCS superposition by Combo score (sum of the ST and raw color overlap) of ligands from PDB codes 3FKT (white) and 2B8L (green).
(b) Aligned enzyme structures ( 3FKT and 2B8L ) with cognate ligands.
Publication Year: 2010
Flavonoids lower Alzheimer's A? production via an NF?B dependent mechanism.
(2011) Bioinformation 6
PubMed: 21738321 | PubMedCentral: PMC3124791 | DOI: null
Overlay of crystal structure of BACE-1 from PDB file 2B8L (brown ribbon) and 2QMF (green ribbon) along with top ranked docked pose of quercetin.
We used GLIDE XP (eXtra Precision release 2010, Schordinger Inc, USA) to perform docking against two different crystal structures of BACE-1 from the PDB files 2B8L and 2QMF.
Overlay of crystal structure of BACE-1 from PDB file 2B8L (brown ribbon) and 2QMF (green ribbon) along with the top ranked docked pose of kaemferol.
Different ligand binding sites (using the following PDB structures: 2B8L, 2QMF, 3CIB, 3L5F, 3KMX) in the BACE-1 catalytic site are indicated by space fill dot representation.
Left Side is a zoom of the active site showing differences in the docking orientation of quercetin in 2B8L (ligand represented by pink sticks) and 2QMF (white sticks).
Figure 4 (A) Graph showing the docking scores (Observed Glide XP score) correlation for the flavonoids between two crystal structures for BACE-1 (2B8L and 2QMF).
Left Side is a zoom of the active site showing differences in the docking orientation of kaempferol in 2B8L (ligand represented by pink sticks) and 2QMF (white sticks).
Publication Year: 2011
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
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, 2P... 6, 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.
Publication Year: 2012
Development of dual inhibitors against Alzheimer's disease using fragment-based QSAR and molecular docking.
(2014) Biomed Res Int 2014
PubMed: 25019089 | PubMedCentral: PMC4075005 | DOI: 10.1155/2014/979606
Docking Studies The 3D structure of human BACE-1 (resolution: 1.70 Å) was obtained from PDB (PDB ID: 2B8L) [ 35 ].
Publication Year: 2014
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