Table 3

The RMSD values of three alignment protocols
Compound Number Pdb ID Ligand RMSD(Å)a RMSD(Å)b RMSD(Å)c pIC50d pIC50e pIC50f
1 1 W51 L01 0.36 0.36 0.645 6.7 7.337 6.72
2 1TQF 32P 0.328 0.409 3.608 5.857 8.627 8.23
3 1YM2 AUA 0.38 0.348 0.95 8.0 7.617 8.34
4 1YM4 AMK 0.305 0.485 2.24 7.41 7.74 7.38
5 2B8V 3BN 0.416 0.47 1.739 7.01 7.27 7.28
6 2F3E AXQ 0.27 0.242 0.676 6.81 7.23 7.26
7 2F3F AXF 0.27 0.344 1.445 6.72 6.69 6.98
8 2IQG F2I 0.398 0.404 0.846 8.3 7.72 7.55
9 2IRZ I02 0.401 0.354 2.219 7.92 8.08 7.24
10 2IS0 I03 0.483 0.556 2.184 6.7 8.05 7.42
11 2OAH QIN 0.857 0.525 2.145 7.96 7.7 7.61
12 2OHL 2AQ 0.144 0.192 0.08 2.7 3.51 3.01
13 2OHM 8AP 0.36 0.468 1.524 3.51 4.12 4.06
14 2OHP 6IP 0.576 0.535 2.432 4.03 4.34 4.22
15 2OHQ 7IP 0.35 0.501 1.29 4.6 5.15 4.27
16 2OHR 8IP 0.297 0.359 2.428 5.0 4.74 4.45
17 2OHS 9IP 0.256 0.314 2.438 5.4 5.06 5.33
18 2OHT IP6 0.455 0.464 1.743 5.04 4.6 5.13
19 2OHU IP7 0.906 0.942 1.921 5.38 5.06 4.87
20 2P83 MR0 0.345 0.363 1.903 7.96 7.54 7.28
21 2PH6 712 0.371 0.563 3.184 7.57 7.97 7.58
22 2B8L 5HA 0.316 0.433 2.51 8.0 8.12 7.72
23 2QZL IXS 0.41 0.4 2.122 8.1 8.68 8.37
24 2ZE1 411 0.825 0.851 0.946 5.25 5.21 5.56
25 2QP8 SC7 0.355 0.342 0.652 8.15 7.61 8.13
26 2VIE VG0 0.396 0.52 1.705 7.48 7.58 7.77
27 2VJ7 VG6 0.765 0.692 2.0 7.31 7.3 7.46
28 2VJ9 VG7 0.413 0.475 1.094 6.74 7.25 7.21
29 2VNM CM8 0.387 0.572 2.457 8.52 8.09 8.3
30 2VNN CM7 0.366 0.333 1.58 8.7 8.0 8.38
31 2WF0 ZY0 0.51 0.527 1.133 6.68 7.25 7.54
32 2WF1 ZY1 0.377 0.361 2.342 8.7 8.19 8.41
33 2ZDZ 310 0.871 0.901 1.642 6.15 5.57 5.95
34 2FDP FRP 0.415 0.428 2.18 7.59 7.13 7.0
35 3CIB 314 0.343 0.355 0.558 7.85 7.58 7.99
36 3CIC 316 0.308 0.291 2.565 8.52 7.62 8.37
37 3CID 318 0.336 0.356 0.816 8.3 7.64 8.37
38 3DM6 757 0.659 0.716 2.814 7.43 8.57 7.88
39 3DUY AFJ 0.443 0.653 1.749 5.85 6.78 6.1
40 3DV1 AR9 0.267 0.251 0.608 6.23 6.61 6.37
41 2P4J 23I 0.614 0.645 4.611 8.96 8.55 8.15
42 3FKT SII 0.596 0.723 1.749 5.55 4.76 6.22
43 2QK5 CS5 0.405 0.392 2.416 7.7 7.63 7.99
44 1XS7 MMI 0.628 0.604 1.37 7.59 7.2 6.47
45 1FKN OM99-2 1.262 1.56 3.3 8.8 8.58 9.03
46 1M4H OM00-3 1.137 1.68 3.9 9.51 9.24 9.3

aProtocol 1. The 46 co-crystallized ligands were aligned in the binding pocket of 1W51 by the superimposition method using the Cα atoms (1W51 structure as the reference). Subsequently, each BACE-1/inhibitor complex (each inhibitor and A chain of 1W51) was energy minimized using the AMBER 9.0 program.

bProtocol 2. The 46 co-crystallized ligands were refined before translocation and energy minimization that was adopted in protocol 1.

cProtocol 3. The 46 co-crystallized ligands were docked into 1W51 using the Surflex program (version 2.11), followed by the energy minimization routine mentioned above.

dexperimental.

epredicted with the 3-PC distance-dependent dielectric constant model (built from a single X-ray crystal structure).

fpredicted with the 5-PC sigmoidal electrostatic model (built from the actual complexes present in the PDB).

Liu et al.

Liu et al. BMC Structural Biology 2012 12:21   doi:10.1186/1472-6807-12-21

Open Data