Table 1. Targets for SPLIF Benchmarking Collected from DUD-E.
| class | target | description | PDB | activesa | decoysa | Gscore cutoffb | refs |
|---|---|---|---|---|---|---|---|
| kinase | FAK1 | focal adhesion kinase 1 | 3bz3 | 100 (71) | 5350 (2131) | –6.0 | (9) (1mp8, 2etm, 2ijm, 3bz3, 4gu6, 4gu9, 4i4e, 4k8a, 4kab) |
| AKT1 | serine/threonine-protein kinase AKT | 3cqw | 293 (199) | 16450 (6131) | –5.0 | (12) (3cqu, 3cqw, 3mv5, 3mvh, 3ocb, 3ow4, 3qkk, 3cql, 3qkm, 4ekk, 4ekl, 4gv1) | |
| protease | ACE | angiotensin-converting enzyme | 3bkl | 282 (277) | 16900 (16454) | –2.5 | (13) (1o86, 1uze, 1uzf, 2c6n, 2oc2, 2xy9, 2xyd, 2ydm, 3bkk, 3bkl, 3l3n, 3nxq, 4bxk) |
| TRYB1 | tryptase beta-1 | 2zec | 148 (59) | 7650 (1657) | –6.0 | (5) (2f9p, 2f9n, 2zeb, 2zec, 4a6l) | |
| HMDH | HMG-CoA reductase | 3ccw | 170 (170) | 8750 (8456) | –2.5 | 22 (1dq8, 1dq9, 1dqa, 1hw8, 1hw9, 1hwi, 1hwj, 1hwk, 1hwl, 2q1l, 2q6b, 2q6c, 2r4f, 3bgl, 3cct, 3ccw, 3ccz, 3cd0, 3cd5, 3cd7, 3cda, 3cdb) | |
| GPCR | ADRB1 | Beta-1 adrenergic receptor | 2vt4 | 247 (240) | 15842 (13932) | –4.0 | (14) (2vt4, 2y00, 2y01, 2y02, 2y03, 2y04, 2ycw, 2ycx, 2ycy, 2ycz, 3zpq, 3zpr, 4ami, 4amj) |
| nuclear receptor | MCR | mineralocorticoid receptor | 2aa2 | 94 (66) | 5150 (2481) | –6.0 | (13) (2aa2, 1y9r, 1ya3, 2a3i, 2aa5, 2aa6, 2aa7, 2aax, 2ab2, 2abi, 2oax, 3vhu, 3vhv) |
| PRGR | progesterone receptor | 3kba | 293 (222) | 15650 (12914) | –5.0 | (17) (1a28, 1e3k, 1sqn, 1sr7, 1zuc, 2ovh, 2ovm, 2w8y, 3d90, 3g8o, 3hq5, 3kba, 3zr7, 3zra, 3zrb, 4a2j, 4apu) | |
| ion channel | GRIK1 | glutamate receptor ionotropic kainate 1 | 1vso | 101 (96) | 6550 (5980) | –2.5 | (17) (1txf, 1vso, 1ycj, 2f34, 2f35, 2f36, 2pbw, 2qs1, 2qs2, 2qs3, 2qs4, 2wky, 3gba, 3gbb, 3s2v, 4dld, 4e0x) |
| synthase | PGH2 | cyclooxygenase-2 | 3ln1 | 435 (374) | 23150 (17948) | –5.0 | 27 (1cvu, 1cx2, 1ddx, 1pxx, 3hs5, 3hs6, 3hs7, 3krk, 3ln0, 3ln1, 3mdl, 3nt1, 3ntb, 3ntg, 3olt, 3olu, 3pgh, 3q7d, 3qh0, 3qmq, 3rr3, 3tzi, 4cox, 4e1g, 4fm5, 4llz, 6cox) |
a
Initial numbers of actives and decoys from DUD-E with the numbers after the Gscore filter included in parentheses.
b
The Gscore cutoffs are set to allow all reference ligands to be retained (in hope to retain the most of actives in the test set as well).