Dimensional Structure of the

Discussion: Molecular Shapes

Instructions

The last discussion’s focus was on Lewis structures. The molecular geometry around each atom can be predicted from Lewis structures. Of course there are variations for bond angles, and some bonds allow for rotation about the bond axis. Therefore, large molecules can adopt complicated shapes. Still, a molecule’s structure is usually important for its function. For this discussion, you will examine how a drug interacts with its target.

  1. Visit the https://www.rcsb.org/
  2. In the menu bar, select Search -> Browse by Annotation.
  3. Click the Anatomical Therapeutic Chemical Classification System link
  4. Find a topic that interests you and continually expand the menus until you come across an interesting drug, then select it (expand by clicking the triangles on the left).
  5. Once you make a selection, you may be presented with several options. Choosing the most relevant option will likely require advance knowledge of biology and biochemistry, but that’s okay. Just choose one (you can limit the interactions to human proteins by choosing Organism: Homo sapiens). For example, I chose the antibacterial drug, tetracycline. I did not choose Homo sapiens, since I know this drug binds to bacterial proteins. To view the structure, click the corresponding link.
    • Screenshot of list of PDB structures that have tetracycline
  6. In most cases, there will be too many atoms. For this discussion, we want to look at how the drug structure interacts with its target. Click on the “Ligand Interaction” link. This will take you to a close-up of the region where the drug binds to its target. Make sure you click the Ligand Interaction link while you are in the Structure Summary tab. You might run into trouble if you click the 3D view button or 3D view tab first, so don’t do this.
    • Screenshot of structure
    • Your view should contain portions with white bonds and portions with grey bonds. The portion with white bonds is the target. The portion with grey bonds is the drug. The positions of the atoms presented are based on experimental data.
  7. To get a feel for the 3 dimensional structure, you can rotate the image and zoom using a mouse. Find a good orientation that shows the drug and take a screenshot.
  8. Finally obtain a picture for the Lewis Structure of only the drug.

For your discussion, provide:

  • The name of the drug and its target (the common name of the drug is preferred).
  • An image of the Ligand View of the drug bound to its target.
  • An image of the Lewis structure of just the drug alone.
  • Give a short description of the drug and what condition it treats.
    • An example of the two images. They were placed side-by-side by first creating a table with 1 row and 2 columns.
    • screenshot of structureTetracycline interaction with E. coli ribosome. lewis structure of tetracyclineLewis structure (abbreviated) of tetracycline.Image Credit: Vaccinationist / Public domain

[If you are interested, tetracycline is an antibacterial drug that binds to bacterial ribosomes. The ribosome is necessary for protein synthesis, and tetracycline inhibits protein synthesis, thereby causing susceptible bacteria to die. The screenshot above shows how tetracycline binds to the ribosome. You may know that humans also have ribosomes in their cells, which are also required for protein sysnthesis. However, the bacterial ribosome and human ribosome are different. Tetracycline binds to bacterial ribosomes, but not to human ribosomes, which makes it an effective antibacterial drug.

Some bacteria have developed a way to become resistant to tetracycline. This resistance system in these bacteria is regulated by a protein that binds to tetracycline. The other entries that came up as results in the initial search show how tetracycline binds to the protein that regulates antibiotic resistance in bacteria.]

Grading

  • (2 pts) Provides the name of the drug and its target.
  • (2 pts) Provides an image that shows how the 3-dimensional structure of the ligand binds to a target
  • (2 pts) Provides an image of the Lewis Structure of the drug
  • (2 pts) Gives a description of the drug and the condition it treats.

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