TABLE 5.
Molecular docking of CviR structures of C. violaceum ATCC 12472 with phenolic compounds found in pulp and seed extracts of S. cumini (L.) Skeels.
| Extract | Compound | PubChem CID |
3QP6 |
3QP8 |
||||
| Binding residue | Score | Rank | Binding residue | Score | Rank | |||
| n.a. | 3-OH-C10-HSL | 71353010 | Y80, W84, Y88, D97, S155 | −85.11 | Y80, W84, Y88, D97, S155 | −81.54 | 1 | |
| n.a. | C10-HSL | 11644562 | Y80, W84, D97, S155 | −82.21 | 2 | Y80, W84, S155 | −81.28 | 2 |
| Pulp | Gallotannins | 452707 | Q70, S82, W84, S89, N92 | −56.34 | 8 | M72, N77, S82 | −75.36 | 3 |
| Pulp | Catechin 3-O-gallate | 5276454 | Y88, S89, N92 | −57.13 | 7 | Y88, N92, A94 | −69.27 | 4 |
| n.a. | C6-HSL | 3462373 | W84, Y80, D97, S155 | −66.92 | 3 | Y80, W84, S155 | −66.69 | 5 |
| Pulp | Rutin | 5280805 | Y80, W84, L85, Y88, S89, D97, T140, S155 | −19.8 | 44 | M72, Y88, N92, A94 | −62.87 | 6 |
| Pulp and seed | Chlorogenic acid | 1794427 | W84, S89 | −64.41 | 4 | W84, S89 | −62.26 | 7 |
| Pulp | Dihydroquercetin | 471 | Y88, S155 | −61.8 | 5 | L85, Y88, S155 | −61.82 | 8 |
| Pulp | Epicatechin 3-O-gallate | 107905 | S89, N92 | −44.49 | 21 | M72, E73, Y88, S89, N92, A94 | −61.27 | 9 |
| Pulp | Epicatechin | 72276 | Y88, D97 | −54.34 | 10 | Y88, D97, M135 | −60.76 | 10 |
| Pulp | Gallocatechin 3-O-gallate | 199472 | Y88, S89, N92 | −46.77 | 17 | Y88, A94 | −60.32 | 11 |
| Pulp | 6-methyldihydroquercetin | 182026 | L85, D97 | −55.21 | 9 | L85, D97 | −59.15 | 12 |
| Pulp | Epigallocatechin 3-O-gallate | 65064 | L85, S89, N92 | −42.62 | 24 | M72, E73, Y88, A94 | −58.81 | 13 |
| Pulp | Peonidin 3,5-diglucoside | 44256843 | Y80, W84, S89, S155 | −1.26 | 47 | M72, V75, Y88, S89, N92, A94 | −58.37 | 14 |
| Pulp | Cyanidin 3-glucoside | 12303203 | Y88, S89, N92 | −52.46 | 12 | Y88, S89 | −57.35 | 15 |
| Pulp | Kaempferol | 5280863 | M135, S155 | −58.54 | 96 | Y80, M135, S155 | −56.46 | 16 |
| Pulp and seed | Quercetin | 5280343 | M135, S155 | −52.95 | 11 | M135, S155 | −53.87 | 17 |
| Pulp | Delphinidin 3-glucoside | 443650 | Y88 | −44.57 | 20 | Y88, S89 | −53.44 | 18 |
| Pulp | Delphinidin 3,5-diglucoside | 10100906 | Y80, S89, T140, S155 | −6.3 | 45 | V75, N77, S89, N92 | −53.39 | 19 |
| Pulp | Petunidin 3-glucoside | 443651 | S89 | −43.63 | 23 | L85, Y88, S89, N92 | −52.67 | 20 |
| Pulp | Cyanidin 3,5-diglucoside | 441688 | Y80, L85, T140, S155 | −6.04 | 46 | V75, Y88, N92, A94 | −52.15 | 21 |
| Pulp | Epigallocatechin | 72277 | L85, Y88, S155 | −50.9 | 14 | W84, L85, Y88, S155 | −52.08 | 22 |
| Pulp | Malvidin 3,5-diglucoside | 44256978 | M72, W84, Y88, S89, N92 | 16.96 | 48 | M72, E73, V75, Y88, S89 | −51.92 | 23 |
| Pulp | Malvidin 3-glucoside | 443652 | S89 | −40.82 | 26 | Y88, S89, A94 | −51.69 | 24 |
| Pulp and seed | Catechin | 9064 | T140, S155 | −52.4 | 13 | Y80, D97, M135, S155 | −51.51 | 25 |
| Pulp | Myricetin 3-glucoside | 44259426 | Y88, S89 | −36.39 | 30 | Y88, S89, N92, A94 | −51.27 | 26 |
| Pulp | Lyricetin 3-rhamnoside | 5281673 | Y88, S89 | −38.57 | 28 | S89 | −51.02 | 27 |
| Pulp | Laricitrin | 5282154 | W84 | −44.09 | 22 | W84 | −49.89 | 28 |
| Pulp | Syringetin | 5281953 | W84 | −42.11 | 25 | W84, S155 | −49.27 | 29 |
| Pulp | Gallocatechin | 65084 | L85 | −50.07 | 16 | L85 | −48.86 | 30 |
| Pulp | Galloyl glucose | 124021 | W84, D97 | −50.28 | 15 | W84 | −48.53 | 31 |
| Pulp | Petunidin 3,5-diglucoside | 10151874 | L85 | −32.86 | 34 | I69, Q70, L85, N92, A94 | −48 | 32 |
| Pulp | Dihydromyricetin | 161557 | – | – | – | S89 | −47.07 | 33 |
| Pulp | Myricetin | 5281672 | – | – | – | W84 | −46.63 | 34 |
| Pulp and seed | Ferulic acid | 445858 | Y80, S155 | −46.05 | 18 | Y80, S155 | −45.85 | 35 |
| Pulp | Myricetin 3-glucuronide | 44259442 | Y88, S89 | −32.82 | 35 | Y88, S89, N92 | −45.78 | 36 |
| Pulp and seed | Ellagic acid | 5281855 | W84 | −39.55 | 27 | W84 | −45.66 | 37 |
| Pulp | Laricitrin 3-glucoside | 44259475 | Y88, S89 | −32.29 | 36 | S89, N92, A94 | −45.42 | 38 |
| Pulp and seed | Caffeic acid | 689043 | M135 | −45.04 | 19 | M135 | −45.18 | 39 |
| Pulp | Myricetin 3-galactoside | 5491408 | Y88, S89, N92 | −35.07 | 32 | Y88, A94 | −45.02 | 40 |
| Pulp | Laricitrin 3-galactoside | 44259474 | Y88 | −30.58 | 37 | Y88, S89 | −43.36 | 41 |
| Pulp | Galloyl (+)-hexahydroxydiphenic acid | 129733714 | W84, D97, Y88, S89, N92 | −29.24 | 39 | L85, Y88, S89, N92, A94 | −43.09 | 42 |
| Pulp | Myricetin 3-pentoside | 21477996 | Y88, S89 | −30.17 | 38 | S89 | −40.98 | 43 |
| Pulp | Syringetin 3-glucoside | 44259492 | S89 | −29 | 40 | S89 | −40.88 | 44 |
| Pulp | Vanillic acid | 8468 | M135, S155 | −38.31 | 29 | S155 | −38.28 | 45 |
| Pulp | Valoneic acid | 71308296 | W84, L85, Y88, D97, S155 | −22.87 | 43 | S82, Y88, S89, N92 | −37.98 | 46 |
| n.a. | Furanone C30 | 10131246 | Y80, T140, S155 | −34.39 | 33 | W84 | −33.6 | 47 |
| Pulp and seed | Gallic acid | 370 | S155 | −35.29 | 31 | S155 | −33.34 | 48 |
| Pulp | Hexahydroxydiphenic acid | 10315050 | L85, Y88, S89, A94 | −23.52 | 42 | L85, S89 | −27.67 | 49 |
| Pulp | Vescalagin (Castalagin) | 168165 | I69, Q70, L85, Y88, S89 | 430.49 | 49 | M72, V75, Y88, S89, A94 | 212.99 | 50 |
| Pulp | Syringetin 3-galactoside | 44259488 | S89, N92 | −27.29 | 41 | – | – | – |
n.a., not applicable; –, the compound did not bind to the CviR protein; Rank, binding affinity scale between CviR protein with 3-OH-C10-HSL, C10-HSL, C6-HSL, furanone C30, and 47 compounds found in pulp and seed extracts of S. cumini (L.) Skeels based on score value. The color of this scale is a color ramp ranging from dark pink (higher affinity) to dark green (lower affinity) and hyphen for no binding. The main results discussed in the text are shown with gray background.