3D Allosteric Modulator Binding

A Rotatable 7-Helix Receptor in Real 3D Space

This companion simulation renders the same allosteric ternary-complex pharmacology as a genuine 3D scene: seven transmembrane helices arranged in a ring that splays outward and shifts color as the receptor's fraction-active population moves toward the R* (active) conformation, exactly as computed by the underlying Black-Leff cooperativity model.

The orthosteric pocket sits at the bundle's core; the allosteric pocket occupies a distinct site on the helix interface — orbiting agonist (blue) and modulator (green for PAM, red for NAM) particles dock into their respective pockets in proportion to concentration, while a live dose-response curve (bottom-right) tracks the same EC50 shift and cooperativity factors (α, β) shown in the readout panel. Drag to orbit the camera around the receptor; scroll to zoom.

Same math, new vantage point

Fraction active, EC50 shift, cooperativity α, and signal output are computed with the identical formulas as the 2D original: a two-cooperativity-factor (α for binding, β for efficacy) ternary complex model with baseline affinities K_A=0.35 and K_B=0.4 for the orthosteric and allosteric sites respectively. A positive allosteric modulator (PAM) increases both factors; a negative allosteric modulator (NAM) decreases them — producing the same leftward/rightward EC50 shift and ceiling/floor saturation behavior described in the 2D model's article sections.