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. 2018 Jun 7;7:e36307. doi: 10.7554/eLife.36307

Figure 7. Fragments cluster at three binding hotspots distal from the active site.

(A) Twenty-four fragments (green) bind to the same site and in similar poses as the BB2 inhibitor (orange, PDB ID 1t49), and similarly displace the α7 helix (foreground, transparent blue, PDB ID 1sug). BB2 is also shown in the following panels to emphasize that its binding site is distinct from the other fragment-binding hotspots. One structure with a fragment bound in this site features a reordered conformation of the α7 helix (pink). (B) Seventeen fragments bind to the L16 site, where they may modulate the conformations of loop 16, the α6 helix, and the protein’s N-terminus on the α1 helix. (C) Thirty fragments bind to the 197 site in one primary subsite contacting K197, or a distinct secondary subsite nearby. The viewing orientation in (A) is as in Figure 1B (‘back side’ of PTP1B), except zoomed in on the BB site (labeled in Figure 1B). The viewing orientation in (B) is also as in Figure 1B, except looking left from the right of that image and zoomed in on the L16 and BB site site. The viewing orientation in A) is as also in Figure 1B, except zoomed in on the 197 site and BB site (labeled in Figure 1B). See also Figure 6E (right) for orientation.

Figure 7—source data 1. Crystallographic statistics for fragment-bound structures.
PDB ID, resolution, Rwork, Rfree, and MolProbity score are listed for the 110 fragment-bound ensemble structures.
elife-36307-fig7-data1.txt (5KB, txt)
DOI: 10.7554/eLife.36307.030
Figure 7—source data 2. Small-molecule fragments tested in enzyme inhibition assays.
These 20 small-molecule fragments, which were thought to bind in or near either the 197 site or the loop 16 site in our structures early in our PanDDA analysis, were tested for inhibition of PTP1B using a pNPP activity assay in quadruplicate with 200 nM protein and 1 mM fragment in 2% DMSO (final). No inhibition was observed compared to no-fragment and no-protein controls.
elife-36307-fig7-data2.txt (1.5KB, txt)
DOI: 10.7554/eLife.36307.031

Figure 7.

Figure 7—figure supplement 1. Fragments overlap with the BB allosteric inhibitor scaffold and suggest possible improvements.

Figure 7—figure supplement 1.

Out of the 24 fragments that bind in the same site as BB2 (PDB ID 1t49, orange), two example fragments (green) are shown that overlap parts of BB2’s pose (asterisks), but also have chemical extensions that may be fruitfully added to the BB scaffold (arrows). (A) The first fragment has aromatic rings in roughly the same positions as does BB2 and a carbon matching a methyl extension in BB2, but in the fragment that carbon is part of two additional protruding rings. (B) The second fragment places two oxygens and a methyl in the same position as the equivalent atom types in BB2, but has a unique ethyl extension.
Figure 7—figure supplement 2. Fragments in the 197 site overlay with glycerols from multitemperature structures.

Figure 7—figure supplement 2.

Fifteen fragments (green) in the primary subsite of the 197 site occupy a similar region of space as ordered glycerols (red) from our 278 K apo structure. The viewing orientation is as in Figure 1B (‘back side’ of PTP1B), except zoomed in on the 197 site (labeled in Figure 1B). See also Figure 6E (right) for orientation.