Expected Preparations:

  Biomolecules:
The molecules of life; The genetic code; Nucleic acids; Amino acids; Protein folding; Post-translational modifications and protein biochemistry; Membrane proteins; Biological function.
   [BIN-SX]
Chimera 		 
  If you are not already familiar with the prior knowledge listed above, you need to prepare yourself from other information sources.   The units listed above are part of this course and contain important preparatory material.  
Keywords: A small-molecule structure tutorial
Objectives:

This unit will …

  • … introduce options to model small molecules;

  • … demonstrate how to find PDB complexes that contain the molecule;

  • … teach how to superimpose model and structure;

 Outcomes:

After working through this unit you …

  • … can model small molecule structures and superimpose them onto cognate molecules in a protein structure ligand binding site.

Deliverables:

Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.

Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don’t overlook these.

Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.

Evaluation:

Evaluation deliverables under revision:
While we are rebalancing formative feedback (advice) and summative feedback (grades) for this course, please ignore all instructions for the submission of assignments until this alert is removed.

 

Contents

Creating with small molecule structures, finding complexes in the PDB that contain the molecule, and superimposing model and structure.

Task…

 

Modeling small molecules

“Small” molecules are solvent, ligands, substrates, products, prosthetic groups, drugs - in short, essentially everything that is not made by DNA-, RNA-polymerases or the ribosome. Whereas the biopolymers are still front and centre in our quest to understand molecular biology, small molecules are crucial for our quest to interact with the inventory of the cell, create useful products, or advance medicine.

A number of public repositories make small-molecule information available, such as PubChem at the NCBI, the ligand collection at the PDB, the ChEBI database at the European Bioinformatics Institute, the Canadian DrugBank, or the NCI database browser at the US National Cancer Institute. One general way to export topology information from these services is to use SMILES strings(W) —a shorthand notation for the composition and topology of chemical compounds.

Task…

Caffeine at PubChem 1. Access PubChem. 1. Enter “caffeine” as a search term in the Compound tab. A number of matches to this keyword search are returned. 1. Click on the top hit - 1,3,7-Trimethylxanthine, the Caffeine molecule. Note that the page contains among other items: 1. # A 2D structural sketch; 1. # An idealized 3D structural conformer, for which you can download coordinates in several formats; 1. # The IUPAC name: 1,3,7-trimethylpurine-2,6-dione; 1. # The CAS identifier 58-08-2 which is a unique identifier and can be used as a cross-reference ID; 1. # The SMILES string(W) CN1C=NC2=C1C(=O)N(C(=O)N2C)C; 1. # … and much more.

Task…

Caffeine at DrugBank 1. Access DrugBank. 1. Enter “Caffeine” in the search form and. . 1. Click on the hit to “Caffeine” itself. Note that the page contains among other items: 1. # A detailed description 1. # A 2D structural sketch with a link to 3D options; 1. # Synonyms, including the IUPAC name: 1,3,7-trimethylpurine-2,6-dione; 1. # … and much more. 1. Follow the link to the 3D options and note the options for downloading information, including the SMILES string and PDB formatted coordinates.

That’s great, but let’s sketch our own version of caffeine. Several versions of Peter Ertl’s Java Molecular Editor (JME)(W) are offered online, PubChem offers this functionality via its Sketcher tool and the PDB has a similar sketching tool on its ligand search page]

Task…

  1. Return to the PubChem homepage.
  2. Click on Draw Structure.
  3. Sketch the structure of caffeine. I find the editor quite intuitive but clicking on the Help button will give you a quick, structured overview. Make sure you define your double-bonds correctly.
  4. Export the SMILES string of your compound to your project folder.

Translating SMILES to structure

ChimeraX can translate SMILES strings to coordinates1.

Task…

  1. Open ChimeraX.
  2. Select Tools ▸ Structure Editing ▸ Build Structure.
  3. In the Build Structure window, select the SMILES string button, paste the string from your file, and click Apply.
  4. The caffeine molecule will be generated and visualized in the graphics window. This is a “stick” representation.
  5. You can rotate it with your mouse, pinch to scale, drag to translate.
  6. Use the Actions ▸ Atoms/Bonds ▸ ball & stick or sphere menu items to change appearance.
  7. Use the Actions ▸ Color ▸ by element menu to change colors.
  8. Change the display back to stick and use Actions ▸ Surface ▸ show to add a solvent accessible surface. Choosing this command triggers the calculation of the surface, which is then available as an individually selectable object. With default pramaters, the surface is a bit rough for this small molecule. Type surface gridSpacing 0.1 to increase the resolution five-fold from its default 0.5A.
  9. By default, the surface inherits the colour of the atoms it envelopes. To change the colour of the surface, use the Actions ▸ Color ▸ all options menu. Click the surfaces button to indicate that the color choice should be applied to the surface object (note what else you can apply color to…), then choose cornflower blue.
  10. Use the Actions ▸ Surface ▸ transparency ▸ 50% menu to see atoms and bonds that are covered by the surface. I find a soft lighting usually works best: lighting soft
  11. To begin working with molecules in “true” 3D, type camera sbs.
  12. Your structure should look somthing like what you see below.

{{Stereo|Caffeine_stereo.jpg|Wall-eye stereo view of the caffeine structure, surrounded by a transparent molecular surface. The image for the left eye is on the left side.}}

Superposition

To investigate a small molecule structure variant in the context of a complex, we need to superimpose it with an existing ligand.

Task…

  • Open the structure 3G6M in ChimeraX. This is one of the hits returned from the PDB search for caffeine - a fungal chitinase for which caffeine is a potent inhibitor.
  • Choose Select ▸ Residue ▸ CFF (CFF is th PDB three-letter code for this hetero compound), then Select ▸ Invert (selected models), Actions ▸ Atoms/Bonds ▸ hide and Actions ▸ Cartoon ▸ hide to show only the caffeine molecules - there are two. Select the one with residue ID 1, and again Actions ▸ Atoms/Bonds ▸ hide. The remaining CFF molecule has residue ID 427.

To superimpose the structures, we can’t use the standard “match” option, because that only works for protein or DNA molecules. Instead, we need to explicitly define matching pairs of atoms through ChimeraX’s command line interface. The command line interface is a very powerful way to issue ChimeraX commands, but it has a bit of a learning curve since we need to use a precise model/residue/atom selection syntax.

  • Open the User hep page and study the select command options. Note how models are specified with a “#” sigil, residues with a “:” or “::” sigil, and atoms with an “@” sigil.
  • The command we need is align, and we need to feed the command atoms in exactly the order of the pairs that the superposition algorithm should superimpose. To identify the atom numbers, we can hover over them with the mouse, or we can select the residue/atom and choose Actions ▸ Label ▸ name. If we superimpose the four nitrogen atoms, the correct command may be:align #,N2,N4,N3 to #2:,N1,N7,N9 to superimpose the model we built from the SMILES string onto the structure - but the exact atom names in the model structure depend on how the SMILES string was written.
  • Note how the two structures are virtually identical - in this case, there are only very small coordinate differences because the conformational degrees of freedom are very much constrained in the xanthin heterocycle. But there are differences nevertheless. One molecule is an idealized structure, the other a structure that has been determined by a high-resolution experiment.
  • Turn the protein structure back on, and study how the ligand is bound.

 

Further Reading

Questions, comments

If in doubt, ask! If anything about this contents is not clear to you, do not proceed but ask for clarification. If you have ideas about how to make this material better, let’s hear them. We are aiming to compile a list of FAQs for all learning units, and your contributions will count towards your participation marks.

Improve this page! If you have questions or comments, please post them on the Quercus Discussion board with a subject line that includes the name of the unit.

References

Page ID: BIN-SX-Small_molecules

Author:
Boris Steipe ( <boris.steipe@utoronto.ca> )
Created:
2017-08-05
Last modified:
2022-09-14
Version:
1.2
Version History:
–  1.2 Edit policy update
–  1.1 2020 Updates - rewrite for changed Websites and using ChimeraX
–  1.0 First live version
–  0.1 First stub
To Do:
–  Be much more prescriptive in what they should do. Discuss isomers, if any and build structure with correct stereo centers. Show molecules separately in superposition, show overview and binding site details. Show pocket surface and side-chains. Show water molecules. Label key interactions and discuss in text. Discuss conformational differences. Could the interqactions be inferred from knowing the model conformation?
Tagged with:
–  Unit
–  Live
–  Evaluated unit
–  Has lecture slides
–  Has further reading

 

[END]

  1. There are also several online servers that translate SMILES strings to idealized structures, for example the online SMILES translation service at the NCI.↩︎