Fig. 6: Applying PocketMiner across the human proteome reveals thousands of cryptic pockets. | Nature Communications

Fig. 6: Applying PocketMiner across the human proteome reveals thousands of cryptic pockets.

From: Predicting locations of cryptic pockets from single protein structures using the PocketMiner graph neural network

Fig. 6

A Though nearly half of proteins lack a pocket in their native, folded state, the majority of these proteins are predicted to have a cryptic pocket. Pie chart shows the number of human proteins containing pockets in their native structures in wheat; proteins that lack pockets in their native structures but are likely to form cryptic pocket(s) in red; and proteins that lack both ground state and cryptic pockets in gray. B Schematic showing proteins involved in the cancer-related Jak/Stat signaling pathway. C The crystal structure of the PIM2 kinase contains an orthosteric binding site but does not reveal any allosteric pockets. D PocketMiner predicts a cryptic pocket at an allosteric site. E Simulations recapitulate a cryptic pocket predicted by PocketMiner. In simulations, a loop peels back to reveal a cryptic pocket (shown in cyan) at the site pinpointed by PocketMiner. The simulated PIM2 structure with a cryptic pocket (orange) is overlaid on the apo PIM2 structure (gray).

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