Getting to know the ICM Graphical User Interface: KRAS-Sotorasib Structural Analysis Example

Reference Video: Exploring the ICM Graphical User Interface

Visualizing Covalent Inhibition: A KRAS G12C Case Study

KRAS functions as a molecular switch, cycling between active (GTP-bound) and inactive (GDP-bound) states to regulate cell signaling. In Non-Small Cell Lung Cancer (NSCLC), the G12C mutation impairs GTP hydrolysis, trapping the protein in a constitutive "on" state that drives oncogenesis. Sotorasib (AMG 510) targets this by binding to a cryptic allosteric pocket beneath the Switch II loop (residues 58-72) specifically during the inactive GDP-bound conformation. Once bound, Sotorasib forms a permanent covalent bond with the mutant Cys12 residue, locking KRAS in the "off" position and effectively silencing the signaling pathway.

Task 1: Read in a PDB file and Convert to an ICM Object

Objective: Import the PDB structure and convert to an ICM object.

• [00:10] Search PDB: Navigate to the Search Tab → Enter 6OIM → Execute search via the Binoculars icon.
• [02:39] Convert to ICM: Right-click the 6OIM object in the Workspace → Select Convert PDB.
  • Configuration: Enable Replace Original and Keep Tight Waters. Confirm with OK.
• Verification: The object prefix in the ICM workspace should now update to ICM.

Task 2: Workspace Navigation & Visualization Tools

Objective: Isolate the binding site, optimize the visual representation and make slides.

• [03:28] Navigation Controls: Utilize the Rotate Mode and graphics window hotspots for precise zooming, rotation and molecule manipulation.

• [04:44] Center on Ligand: Double-click the ligand identifier (e.g., amov) in the Workspace tree and click on the center button.

• [01:57] Residue Identification: Use the Pick Residue Selection button to highlight Cys12 at the covalent attachment site. A text residue label is automatically applied using this option - you can modify font color and size by clicking and holding on the Residue label button in the Display tab.

• [05:21] Change Color of Ligand Carbon Atoms: Select the ligand in the ICM workspace (double click) and then click and hold the Stick button in the Display Tab → Choose Color C → Select Green. This preserves standard CPK colors for heteroatoms.
• [05:44] (Un)Display Molecules using the ICM Workspace: Toggle the Undisplay buttons to hide GDP and Waters, focusing the view on the primary pocket.

• [06:09] Save Slides: Click the Camera Icon at the footer of the graphics window to save the current orientation as a Slide. Read more here...

Task 3: Molecular Interaction Mapping

Objective: Identify the covalent linkage and key non-covalent anchors.

• [05:00] Interaction Analysis: Right-click the ligand → Display Pocket → Ligand Pocket Interactions.
• [06:34] Display Tuning: Use the +/- buttons in the Display Tab to adjust the thickness of interaction dashes for better visibility.
• [09:22] 2D Topology: Right-click ligand → Advanced → Tools → Ligand 2D Diagram to generate a flat map of interactions.

Task 4: Structural Dynamics & Surface Modeling

Objective: Characterize mobile loops and electrostatic pocket properties.

• [07:22] Switch II Loop Selection: In the sequence viewer, click-drag to select residues 58 through 65.
• [07:50] Highlighting Regions: Apply a Magenta Ribbon to the selection to differentiate the mobile loop from the protein core.
• [08:25] Pocket Property Mesh: Right-click ligand → Display Pocket → Receptor Pocket Mesh.
  • Legend: Blue (Donor), Red (Acceptor), Green (Hydrophobic).

Task 5: Comparative Superposition

Objective: Evaluate conformational changes between bound and apo states.

• [10:19] Load Reference: Fetch PDB 4OBE (Closed state).
• [11:08] Structural Alignment:
  • Select Chain A for both 6OIM and 4OBE in the Workspace (Ctrl/Cmd + Click).
  • Navigate to Display Tab → Superimpose.
• [11:54] Differential Analysis: Observe the shift in the Switch II loop (Magenta) required to accommodate the inhibitor.