Table 2 Details and parameter settings of molecular docking
| Â | Protein | PDB ID | Targeting small molecules | Docking center (x,y,z) | Protein pocket size (x,y,z) |
|---|---|---|---|---|---|
Proteins with corresponding targeting small molecules | TLR4 | 3ULA | Stepharine [44] | 35.5,23.2,2.0 | 31.9,27.5,25.1 |
NOS2 | 4NOS | S-ethylisothiourea [45] | −1.8,97.7,20.4 | 13.1,14.1,12.1 | |
TGFB1 | 1KLC | Disitertide [46] | 9.4,0.0,0.0 | 26.7,30.0,10.0 | |
NFKB1 | 1NFK | Kamebakaurin [47] | 0.4,-0.1,0.2 | 18.8,16.2,14.5 | |
TP53 | 2X0U | J-518147 [48] | 124.9101.8,44.8 | 12.4,15,2,17.2 | |
MIF | 1LJT | ISO-1 [49] | −40.9,40.4,7.5 | 16.7,16.7,18.8 | |
SYK | 3SRV | GSK143 [50] | 0.0,-1.7,-27.3 | 19.6,16.8,17.1 | |
MMP9 | 4XCT | N73 [51] | 18.4,-17.1,19.7 | 15.4,20.5,18.1 | |
PPARG | 1FM6 | Rosiglitazone maleate [52] | 17.0,-21.1,11.8 | 19.9,20.2,16.7 | |
XIAP | 5M6H | AT-IAP [53] | −13.4,-18.6,-5.0 | 18.9,20.7,21.7 | |
PTGS2 | 1PXX | Diclofenac [54] | 27.1,24.3,14.7 | 15.4,16.7,16.5 | |
STAT3 | 6NUQ | SD36 [55] | 13.6,54.0,-0.1 | 19.8,30.6,22.0 | |
TNF | 2AZ5 | SPD304 [56] | −19.2,74.5,33.8 | 19.1,18.2,18.5 | |
CHRNA7 | 3SQ6 | GTS21 [57] | 2.7,4.6,-0.1 | 19.0,24.0,12.9 | |
PIK3CG | 2A4Z | AS-604850 [58] | 44.0,14.3,32.0 | 19.4,13.9,16.5 | |
IL2 | 1QVN | SP4206 [59] | 16.8,17.7,81.4 | 20.2,29.2,25.9 | |
MAPK14 | 6SFO | SR-138 | 0.0,1.1,-19.2 | 20.4,16.9,25.8 | |
AKT1 | 3O96 | Akt inhibitor VIII [60] | 9.7,-7.8,10.6 | 17.7,25.8,22.3 | |
Proteins with eutectic ligands | IL6 | 1ALU | NA | −7.7,-12.7,0.0 | 15.1,13.9,12.4 |
CCR1 | 7VL8 | NA | 120.6120.7124.4 | 15,20.5,24.5 | |
IL4R | 3BPN | NA | 12.0,8.5,42.9 | 16.9,15.6,12.7 | |
VEGFA | 6ZFL | NA | 22.9,19.4,2.2 | 13.7,15.6,15.7 | |
ICAM1 | 1MQ8 | NA | −16.3,41.0,-20.9 | 17.9,12.2,14.4 | |
IFNG | 6E3L | NA | −2.7,-6.9,-11.9 | 15.6,16.5,13.0 | |
IL1B | 6Y8I | NA | 7.5,25.5,7.1 | 19.8,14.2,13.8 | |
CXCL8 | 6WZM | NA | 23.9,-2.1,31.3 | 14.3,17.0,16.4 | |
CXCL2 | 5OB5 | NA | −3.2,20.1,-22.7 | 12.5,12.2,13.2 | |
Blind docking protein | CCL2 | 1DOk | NA | 14.526,49.282,33.197 | 58.373,40.999,39.281 |
CXCL10 | 1O7Y | NA | 49.12,8.793,8.502 | 45.099,49.176,51.687 | |
STAT1 | 1YVL | NA | −10.34,-26.601,166.516 | 102.488,95.296,149.498 | |
IL1A | 2L5X | NA | 35.574,-1.905,-0.757 | 37.913,47.5,35.205 | |
SPP1 | AF-P10451-F1 | NA | −15.373,-2.209,8.391 | 135.821,88.635,139.822 | |
IL10 | 2H24 | NA | 15.516,22.87,3.383 | 45.294,38.699,73.842 | |
CD14 | 4GLP | NA | 44.923,57.035,-3.18 | 30,30,30 |