Chemistry Reference
In-Depth Information
(a)
(b)
7500
7000
6500
6000
5500
5000
4500
4000
3500
3000
0
1
2
3
4
5
6
7
RMSD TO TARGET
Figure 5.3
(A) COST versus the RMSD (Å) to the target pose for mFABP/
1
obtained with
SDM
0.50 and with the predicted protein chemical shifts set to the corresponding BMRB
average values. (B) Superposition of target pose and the minimum cost pose (dark gray) from (A).
=
of 1500 trial poses were generated for LFA-1/
2
, with minimum and maximum RMSDs
to the trial pose of 0.22 and 8.52 Å, respectively. Some limited sampling of the protein
conformation was used in this case. The experimental 3D X-filtered NOESY spectrum
(
τ
m
=
100 ms) for this complex yielded 69 peaks, which were clustered into 51 protein
1
H
13
C groups. It is important to note that the hydantoin core of
2
did not yield any protein-
ligand NOEs. Results for LFA-1/
2
(SDM
=
0.25) are shown in Figure 5.4 (
r
=
0.858
between COST and RMSD).
(a)
(b)
8000
7000
6000
5000
4000
0
1
2
3 4
RMSD TO TARGET
5
6
7
8
9
Figure 5.4
(A) COST
pose
versus the RMSD (Å) to the target pose for LFA-1/
2
, with SDM
0.25
and with the predicted protein chemical shifts set to the corresponding BMRB average values.
(B) Superposition of the target pose and the minimum cost pose (dark gray) from (A).
=
