Table 1.
Docking for TRI5 containing the inorganic pyrophosphate (PPi).
| PPi | |||||
|---|---|---|---|---|---|
| Tested Ligands | % | Sites | E.F.E.B. a | E.I.C., Ki b | Interaction with Amino Acids |
| p-Coumaric acid 1 | 75 | c.d. c | −13.23 | 199.19 pM | Asp100 Glu164 Pro178 Leu181 Arg182 Asn185 Asp239 Ile241 Ser242 Leu243 Asn246 PPi700 Mg702 Mg703 |
| 1 | c.d. | −7.73 | 2.17 uM | Ile70 Met73 Tyr93 Leu97 Asp100 Phe157 Arg182 Asn185 Leu187 PPi700 Mg703 | |
| 4 | 3 | −5.59 | 79.22 uM | Met1 Glu2 Asn3 Phe4 Thr6 Phe234 Asp235 Lys313 | |
| 11 | 3 | −5.56 | 84.50 uM | Phe4 Thr6 Tyr231 Phe234 Asp235 Arg306 Lys313 | |
| Caffeic acid 2 | 39 | c.d. | −12.06 | 1.45 nM | Asp100 Glu164 Leu181 Arg182 Asn185 Asp239 Ile241 Ser242 Leu243 Asn246 PPi700 Mg702 Mg703 |
| 16 | 4 | −5.81 | 55.08 uM | Met55 Leu56 Lys57 Arg62 Val98 Ser102 Ser103 Pro126 Trp127 | |
| 11 | 3 | −5.45 | 101.75 uM | Met1 Glu2 Asn3 Phe4 Thr6 Thr231 Phe234 Asp235 Lys313 | |
| Ferulic acid 3 [32] | 2 | c.d. | −9.62 | 89.12 nM | Asp100 Glu164 Leu181 Arg182 Asn185 Asp226 Glu233 Arg238 Asp239 Ser242 Leu243 Asn246 PPi700 Mg703 |
| 6 | c.d. | −7.78 | 1.99 uM | Ile70 Met73 Tyr93 Thr96 Asp100 Phe157 Arg182 Asn185 Leu187 PPi700 Mg703 | |
| 13 | 3 | −5.58 | 80.65 uM | Met1 Glu2 Asn3 Phe4 Tyr231 Lys232 Phe234 Asp235 Arg306 | |
| 8 | 4 | −5.51 | 92.16 uM | Met55 Leu56 Lys57 Arg62 Val98 Ser102 Ser103 Pro126 Trp127 | |
| 14 | 3 | −5.48 | 96.45 uM | Phe4 Thr6 Tyr231 Phe234 Asp235 Arg306 Lys313 | |
| 19 | 5 | −5.19 | 157.79 uM | Gln53 Gln54 Leu56 Lys57 Val58 Pro60 Leu63 | |
| Propyl gallate 4 [32] | 40 | 1 | −5.86 | 50.71 uM | Ala65 Gln68 Thr69 Tyr76 Trp298 Cys301 Asp302 Ala303 Gly336 Val338 Pro340 Trp343 |
| 13 | 2 | −5.28 | 133.84 uM | Leu300 Cys301 Asp302 Ala303 Arg306 Leu307 His308 Phe329 Ala333 Ala337 | |
| Octyl gallate 5 | 12 | 2-1 | −6.42 | 19.85 uM | Gly72 Tyr76 Leu300 Cys301 Asp302 Ala303 Arg306 Leu307 His308 Phe329 Gly336 Ala337 Val338 |
| 9 | 1 | −6.30 | 23.91 uM | Ala65 Ser66 Gln68 Thr69 Tyr76 Cys301 Asp302 Ala303 Arg304 Gly336 Val338 Trp343 | |
| 16 | 1-2 | −6.28 | 24.94 uM | Gln68 Thr69 Gly72 Cys301 Asp302 Ala303 Leu307 His308 Phe329 Gly336 Ala337 Val338 Trp343 | |
| 5 | 1-2 | −5.83 | 53.08 uM | Leu36 Gly72 Tyr76 Leu300 Cys301 Asp302 Ala303 Arg306 Leu307 His308 Gly336 Val338 Trp343 | |
| Carvacrol 6 | 48 | 1 | −5.31 | 127.65 uM | Leu36 Gln68 Thr69 Gly72 Tyr76 Cys301 Asp302 Gly336 Ala337 Val338 Trp343 |
| 21 | 2 | −5.29 | 132.10 uM | Leu300 Cys301 Asp302 Ala303 Arg306 Leu307 His308 Phe329 Ala333 | |
| 11 | c.d. | −5.27 | 136.69 uM | Met73 Tyr93 Thr96 Leu97 Asp100 Phe157 Leu187 Val191 Met221 | |
| 16 | 4 | −5.18 | 160.32 uM | Met55 Lys57 Arg62 Val98 Leu99 Ser102 Asp104 Pro126 Trp127 | |
| Thymol 7 | 5 | c.d. | −5.63 | 74.28 uM | Glu164 Pro178 Leu181 Arg182 Asn185 Asp226 Glu233 Ile241 Ser242 Leu243 Asn246 PPi700 |
| 20 | 4 | −5.50 | 92.72 uM | Met55 Leu56 Lys57 Val58 Val98 Leu99 Asp104 His125 Pro126 Trp127 | |
| 58 | 1 | −5.34 | 121.84 uM | Tyr76 Trp298 Cys301 Asp302 Gly336 Val338 Pro340 Trp343 | |
| 10 | c.d. | −5.17 | 161.91 uM | Ile70 Met73 Tyr93 Thr96 Leu97 Asp100 Phe157 Leu187 Val191 PPi700 | |
| R-Linalool 8 | 36 | 1 | −5.32 | 126.02 uM | Leu36 Gln68 Thr69 Gly72 Tyr76 Cys301 Asp302 Gly336 Ala337 Val338 Trp343 |
| 21 | c.d. | −5.31 | 128.71 uM | Ile70 Met73 Trp78 Tyr93 Thr96 Leu97 Phe157 Leu187 Val191 Met221 Tyr295 | |
| 12 | 1 | −5.24 | 145.29 uM | Leu36 Ala65 Gln68 Thr69 Gly72 Tyr76 Asp302 Ala303 Trp343 | |
| 10 | 4 | −5.07 | 193.14 uM | Met55 Leu56 Lys57 Val98 His125 Pro126 Trp127 | |
| S-Linalool 8 | 11 | 4 | −5.26 | 140.56 uM | Met55 Leu56 Lys57 Arg62 Val98 His125 Pro126 Trp127 |
| 36 | 1 | −5.22 | 148.58 uM | Gln68 Thr69 Tyr76 Cys301 Asp302 Gly336 Val338 Pro340 Trp343 | |
| 27 | c.d. | −5.18 | 160.63 uM | Ile70 Met73 Trp78 Tyr93 Thr96 Leu97 Val191 Met221 Tyr295 | |
| 17 | 1 | −5.14 | 171.53 uM | Ala65 Gln68 Thr69 Gly72 Tyr76 Cys301 Asp302 Ala303 Trp343 | |
| Geraniol 9 | 2 | c.d. | −6.60 | 14.53 uM | Pro178 Leu181 Arg182 Asn185 Glu233 Arg238 Asp239 Ile241 Ser242 Leu243 Asn246 PPi700 Mg702 MGg703 |
| 12 | 2 | −5.42 | 106.54 uM | Leu300 Cys301 Asp302 Ala303 Tyr305 Arg306 Leu307 His308 Glu309 Phe329 | |
| 47 | 1 | −5.30 | 131.30 uM | Gln68 Thr69 Gly72 Tyr76 Cys301 Asp302 Gly336 Ala337 Val338 Pro340 Trp343 | |
| 16 | c.d. | −5.04 | 200.93 uM | Ile70 Met73 Tyr93 Thr96 Leu97 Phe157 Arg182 Leu187 Met221 Asn225 Tyr295 Trp298 Tyr305 PPi700 | |
| Apocynin 10 [32] | 4 | c.d. | −6.86 | 9.29 uM | Asp100 Glu164 Arg182 Asn185 Asp226 Glu233 Arg238 Asp239 Ser242 Leu243 PPi700 Mg703 |
| 60 | 1 | −5.35 | 119.64 uM | Gln68 Tyr76 Cys301 Asp302 Gly336 Ala337 Val338 Trp343 | |
| 11 | 1 | −5.25 | 134.28 uM | Gln68 Tyr69 Gly72 Tyr76 Trp298 Cys301 Asp302 Gly336 Ala337 Val338 | |
| Eugenol 11 [32] | 3 | c.d. | −5.65 | 72.36 uM | Asp100 Glu164 Leu181 Arg182 Asn185 Asp226 Glu233 Arg238 Asp239 Ile241 Ser242 Leu243 Asn246 PPi700 |
| 31 | 2 | −5.12 | 177.48 uM | His299 Leu300 Cys301 Asp302 Ala303 Arg306 Leu307 His308 Glu309 Phe329 | |
| 19 | 2 | −5.07 | 193.10 uM | His299 Leu300 Cys301 Asp302 Ala303 Arg306 Leu307 His308 Phe329 Ala333 Ala337 | |
| 22 | 1 | −4.98 | 224.72 uM | Gln68 Thr69 Tyr76 Trp298 Cys301 Asp302 Gly336 Ala337 Val338 Trp343 | |
| Magnolol 12 [32] | 29 | 1 | −6.91 | 8.56 uM | Gln68 Thr69 Gly72 Tyr76 Leu300 Cys301 Asp302 Phe329 Gly336 Ala337 Val338 Pro340 |
| 11 | 1-2 | −6.49 | 17.43 uM | Leu36 Gly72 Tyr76 Trp298 Leu300 Cys301 Asp302 Ala303 Phe329 Ala333 Ala337 Val338 Pro340 Trp343 | |
| 14 | 4 | −5.91 | 46.77 uM | Met55 Leu56 Lys57 Val58 Arg62 Val98 Ser102 Ser103 Pro126 Trp127 | |
| Honokiol 13 | 25 | 1-2 | −7.25 | 4.81 uM | Gln68 Thr69 Gly72 Trp298 Leu300 Cys301 Asp302 Phe329 Ala333 Ala337 Val338 Trp343 |
| 6 | 2 | −7.15 | 5.72 uM | Leu300 Cys301 Asp302 Ala303 Tyr305 Arg306 Leu307 His308 Tyr311 Phe329 Glu330 Ala333 Ala337 | |
| 24 | 1-2 | −7.04 | 6.91 uM | Ala65 Gln68 Thr69 Gly72 Tyr76:Trp298 Cys301 Asp302 Ala303 Gly336 Ala337 Val338 Pro340 | |
| 16 | 1-2 | −6.92 | 8.44 uM | Gln68 Thr69 Gly72 Tyr76 Trp298 Cys301 Asp302 His308 Ala337 Val338 | |
| Eugenol dimer 14 [32] | 14 | 1-2 | −6.69 | 12.41 uM | Gln68 Gly72 Tyr76 Trp298 Cys301 Asp302 Ala303 His308 Ala337 Val338 |
| 28 | 1-2 | −6.67 | 12.98 uM | Thr69 Gly72 Tyr76 Trp298 Leu300 Cys301 Asp302 Ala303 Phe329 Ala333 Ala337 Val338 Ala339 Pro340 Trp343 | |
| 10 | 1-2 | −6.27 | 25.41 uM | Leu36 Gln68 Thr69 Tyr76 Leu300 Cys301 Asp3Ala303 Phe329 Ala333 Gly336 Ala337 Val338 Trp343 | |
| 14 | 4 | −5.41 | 108.76 uM | Lys57 Val58 Arg62 Val98 Leu99 Ser102 Ser103 Asp104 Pro126 Trp127 | |
| Ferulic acid dimer 15 | 4 | 1-2 | −6.48 | 17.71 uM | Leu36 Ala65 Gln68 Thr69 Gly72 Tyr76 Cys301 Asp302 Ala303 Arg304 Ala337 Pro340 Trp343 |
| 26 | 2-1 | −5.55 | 85.48 uM | Gln68 Thr69 Tyr76 Trp298 Cys301 Asp302 Ala303 Gly336 Ala337 Val338 Ala339 Pro340 | |
| NPD352 | 6 | 1-2 | −9.52 | 104.59 nM | Tyr76 Cys301 Asp302 Ala303 His308 Tyr311 Phe329 Glu330 Ala333 Ala337 Val338 Pro340 Trp343 |
| 22 | 1-2 | −8.05 | 1.25 uM | Gly72 Tyr76 Cys301 Asp302 Ala303 His308 Phe329 Ala333 Ala337 Val338 Ala339 Trp343 | |
a E.F.E.B.: Estimated Free Energy of Binding, b E.I.C., Ki: Estimated Inhibition Constant, Ki., c c.d.: catalytic domain.