Zn2+ mediated ligand binding in thrombin

For these three ligands crystal structure with Zn2+ mediated bound ligands are available but not without Zn. The experimental determined Ki values showed large differences between assays with and without Zn. The docking of those ligands was performed without Zn and the predicted deltaG values are quite close to the experimental ones measured without Zn. The question was then, whether it is possible to model the coordination of the Zn and the influence on the predicted deltaG.
In the first step, the X-ray conformations were used without Zn, but the predicted deltaG didn't show any higher binding affinity. Then the thrombin structures (HIP57 was changed to HID) were minimized together with one Zn ion (high constrain) and the ligand. The ligand and Zn were used as one residue in ANAL for calculating interaction energies. Because of some problems with UHBD, the desolvation energy terms for the ligand and protein were taken from the calculation using the X-ray conformations without Zn. This resulted in even a lower binding affinity. Finally, the lowest deltaG were predicted for docked ligands (best deltaG desolv).

ligand
 PDB
 deltaG exp
 deltaG exp pred deltaG,
w/o variable selection,
LV4



EDTA
 Zn2+
 X-ray w/o Zn
 X-ray with fixed Zn docking
best deltaG desolv
(UHBD) ranked
A49
 1c1u
 -7.7
 -11.2
 -7.3
 -6.3
 -8.7
A58
 1c1v
 -7.4
 -10.4
 -5.6
 -4.8
 -7.0
A59
 1c1w
 -4.1
 -9.7
 -5.9
 n.d.
 -6.6
in kcal/mol

Figure: Minimized ligand A49 with thrombin model 3 (HIP57 - HID) and a Zn ion (high constrain).
1c1u/A49 - thrombin model 3/HID - Zn

COMBINE model: ~/combine2go/data/thrombin/model3_180506/anal2/output-A12_1-A09-A84-A88-A89-A90.dat
without variable selection, best Q2 at LV 4:

X-ray structures without Zn

External PLS predictions for /home/henricsn/report/COMBINE-paper/structure-figure/Zn-selectivity/thr-1c1w-1c1u-1c1v.dat
1 A49.0
Exper: -7.688 Pred:( 1 ) -6.958 ( 2 ) -7.111 ( 3 ) -7.076 ( 4 ) -7.306 ( 5 ) -7.38

2 A58.0
Exper: -7.406 Pred:( 1 ) -6.596 ( 2 ) -5.771 ( 3 ) -5.159 ( 4 ) -5.59 ( 5 ) -5.582

3 A59.0
Exper: -4.09 Pred:( 1 ) -6.761 ( 2 ) -5.841 ( 3 ) -5.374 ( 4 ) -5.902 ( 5 ) -5.863

Y_1 Components SDEP (external)
0 3.2586
1 1.6651
2 1.4222
3 1.5354
4 1.4972
5 1.4794

X-ray structures with fixed Zn

Interaction energies of ligand and Zn (handled as one residue) and desolvation terms of the ligand alone

External PLS predictions for /home/henricsn/report/COMBINE-paper/structure-figure/Zn-selectivity/Zn/output.dat
1 A49.0
Exper: -7.688 Pred:( 1 ) -7.182 ( 2 ) -8.015 ( 3 ) -8.377 ( 4 ) -6.263 ( 5 ) -5.666

2 A58.0
Exper: -7.406 Pred:( 1 ) -6.94 ( 2 ) -6.966 ( 3 ) -6.901 ( 4 ) -4.763 ( 5 ) -4.009

Y_1 Components SDEP (external)
0 1.6734
1 0.4861
2 0.3879
3 0.6039
4 2.1231
5 2.7953

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