Sandbox Reserved 429

Outline of Topics:

• Secondary Structure Elements
• Location and organization
• Polar and Non-polar Groups
• Location and organization
• Identify Hinge Location (Connects Sub-units)
• Identify Cystine Bonded to Ligand

If you look at the , you see that most residues are Polar and not as many are Non-polar.

Binding Interactions

LRRK2 contains binding sites for 6-[(2,5-dimethoxyphenyl)sulfanyl]-3-(1-methyl-1H-pyrazol-4-yl)[1,2,4]triazolo[4,3-b]pyridazine which we will refer to by its PDB code, 2YK.

The residues involved in binding interactions are listed below:

• LEU 903A
• VAL 911A
• GLY 1040A
• GLU 979A
• VAL 981A

These residues are highlighted in green and the ligand 2YK is shown in blue.

The scene below provides an alternative view of the binding interactions with the residues labelled in red with their corresponding number and the ligand, 2YK, labelled in blue.

Additional Features

Quiz Question 1

Quiz Question 2

For our second question I am going to present a green scene with the binding pocket and the ligand shown. The green scene will show the details of the binding pocket including the secondary structures and the residues which make them up. I will then ask the student to think about the scene and give three alternations to the ligand which would make it a better competitive inhibitor.

See Also

• [2ZEJ]
• [Leucine-rich Repeat]
• [Crystal structure of a leucine-rich repeat protein]
• [Leucine-rich repeat-contain protein 4]
• [[1]]

Credits

Introduction - Megan Greiner

Overall Structure - Nick Barberio

Drug Binding Site - John Vetrano

Additional Features - Nicole Garvin

Quiz Question 1 - Charit Tippareddy

Quiz Question 2 - Peter Kelly

References