Table 4.
Summary of difference between interaction of ligands with protein complex in XP docking and induced fit docking
| Ligands | Interaction shown in XP docking | Interaction shown in induced fit docking |
|---|---|---|
| Favipiravir |
H-bond: Phe E 497, Tyr E 453, Tyr E 505. Hydrophobic interaction Charged negative: Asp A 38. Charged positive: Lys A 353, Lys E 403. Hydrophobic: Tyr E 495. Polar: Gln E 498, Gln E 493, Ser E 494, Asn E 501, His A 34 |
H-bond: Gly E 496, Lys E 403, Tyr E 505. Salt bridge: Lys E 403. Hydrophobic interaction Charged negative: Asp A 38, Glu A 37. Charged positive: Lys A 353. Hydrophobic: Tyr E 495, Tyr E 449, Tyr E 453, Phe E 497. Polar: Asn E 501, Gln E 493, Ser E 494, Asn E 501, His A 34 |
| Ribavirin |
H-bond: Gly E 496, His A 34, Tyr E 453, Tyr E 505. Hydrophobic interaction Charged negative: Glu A 37, Asp A 38. Charged positive: Lys A 353, Lys E 403, Arg A 393. Hydrophobic: Tyr E 495, Phe E 497. Polar: Asn E 501, Gln E 506, Gln E 498, Gln E 493, Ser E 494, Asn A 33 |
H-bond: Ser E 494, Asn E 501, Tyr E 505, Lys A 353, His A 34. Hydrophobic interaction Charged negative: Glu A 37, Asp A 38, Glu A 35. Charged positive: Lys A 353, Lys E 403. Hydrophobic: Tyr E 495, Phe E 497, Tyr E 449, Tyr E 453. Polar: Gln E 506, Gln E 498, Gln E 493 |
| Iso-chlorogenic |
H-bond: Gly E 496, Val E 417, Asp E 406, His A 34 Salt bridge: Arg E 408. Hydrophobic interaction Charged negative: Asp E 405, Glu A 37, Asp A 38. Charged positive: Lys A 353, Lys E 403. Hydrophobic: Ile E 418, Tyr E 495, Tyr E 505, Tyr E 449, Tyr E 453. Polar: Gln E 409, Gln E 493, Ser E 494 |
H-bond: Asn A 33, Gln A 388, Tyr E 453, His A 34, Lys E 403, Gly E 496. Salt bridge: Lys E 403. Hydrophobic interaction Charged negative: Glu E 35, Glu A 37, Asp A 38. Charged positive: Lys A 353, Arg A 393. Hydrophobic: Phe A 390, Pro A 389, Ala A 387, Ala A 386, Ala A 36, Tyr E 495, Phe E 497, Tyr E 505. Polar: Gln E 493, Ser E 494 |
| Taxiphyllin |
H-bond: Arg A 393, Ala A 348, Ash A 350. Hydrophobic interaction Charged negative: Glu A 37, Asp A 382. Charged positive: Lys A 353. Hydrophobic: Trp A 349, Leu A 351, Phe A 40, Tyr A 385, Phe A 390. Polar: Hie 401, Asn A 394 |
H-bond: Arg A 393, Tyr E 505, Tyr E 453, Gly E 496. Hydrophobic interaction Charged negative: Glu A 37, Asp A 38. Charged positive: Lys A 353, Lys E 403. Hydrophobic: Phe A 390, Tyr E 449, Tyr E 495, Phe E 497, Pro A 389. Polar: Gln A 388, Asn A 33, His A 34, Ser E 494, Asn E 501 |
| Vasicine |
H-bond: Arg A 393, Asn A 394 Pi cation: Phe A 390, Phe A 40. Hydrophobic interaction Charged negative: Ash A 350, Glu A 37 Charged positive: Lys A 353 Hydrophobic: Leu A 391, Tyr A 385, Leu A 351 |
H-bond: Arg A 393, Asn A 394Pi cation: Phe A 390, Phe A 40.Pi–Pi stacking: Phe A 390Hydrophobic interaction Charged negative: Ash A 350, Glu A 37 Charged positive: Lys A 353 Hydrophobic: Leu A 391, Tyr A 385 |
| ( +)-Catechin |
H-bond: Leu A 391, Arg A 393, Ash A 350. Hydrophobic interaction Charged positive: Lys A 353. Hydrophobic: Phe A 40, Leu A 351, Phe A 390, Ala A 99, Leu A 73, Trp A 69. Polar: Asn A 394 |
H-bond: Ala A 386, Thr A 324, Gly A 354, Asp E 405. Pi–Pi stacking: Tyr E 505. Hydrophobic interaction Charged positive: Lys E 403, Arg A 393. Hydrophobic: Ala A 387, Val E 503, Phe A 356. Polar: Gln A 388 |
| Caffeic Acid |
H-bond: Gly E 496.Salt bridge: Lys E 403 Hydrophobic interaction Charged negative: Asp E 406, Glu A 37, Asp A 38. Charged positive: Lys A 353 Hydrophobic: Tyr E 453, Tyr E 505, Tyr E 495, Phe E 497 Polar: His A 34 |
H-bond: His A 34, Asp A 38, Gly E 496, Lys E 403 Salt bridge: Lys E 403 Pi–Pi stacking: Phe A 274.Hydrophobic interaction Charged negative: Asp E 406, Glu A 37, Asp A 269 Charged positive: Lys A 353, Lys A 441, Arg A 273. Hydrophobic: Tyr E 453, Tyr E 505, Tyr E 495, Leu A 267, Leu A 444, Ile A 446, Val A 447, Trp A 275, Val E 471 Polar: Gln A 442, Thr A 445, Thr A 276, Thr A 449 |