I was tried to dock Cucurbit[7]uril with protein in Autodock vina, but the ligand structure i.e., the structure of Cucurbit[7]uril was planar (taken from the pubchem or other website everywhere the same planar structure was available), whether in all the research papers the pumpkin like 3D structure having a cavity to interact with the guest molecule were reported. I am very new in this field, so, I could not convert it to the 3D structure. Can anyone help me to solve this problem? It will be very helpful to me.
You can find the experimental structure on CCDC
https://www.ccdc.cam.ac.uk/structures/Search?Compound=Cucurbit%5B7%5Duril&DatabaseToSearch=Published
e.g. entry CABVUZ (4-(2-(4-(Dimethylamino)phenyl)diazeniumyl)benzenesulfonate cucurbit[7]urilhydrate)
from https://www.sciencedirect.com/science/article/abs/pii/S0022286015304439?via%3Dihub
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