Table 2.
Docking results of heparin and LMW heparin derivatives with T7RNAP.
| SL NO. | COMPOUND NAME | XP G-SCORE (kcal/mol) | H-BOND INTERACTIONS D-A[X]a | METAL-LIGAND INTERACTIONS M-A[X]a | HYDROPHOBIC INTERACTIONS |
|---|---|---|---|---|---|
| 1 | Heparin | −11.86 | NH1(Arg 425)-O28[2.88] | MG884-O38[2.76] | Asp 506, Met 635, Thr 636, Ala 638, Pro 780, His 811. |
| OD1(Asn 466)-O43[2.64] | MG885-O13[2.28] | ||||
| OD2(Asp 537)-O38[2.57] | MG885-O35[2.16] | ||||
| OG (Ser 541)-O30[2.73] | |||||
| OH(Tyr 571)-O41[3.16] | |||||
| NH1(Arg 632)-O47[3.00] | |||||
| NH1(Arg 632)-O14[3.04] | |||||
| OD1(Asp 653)-O53[2.82] | |||||
| NE2(His 784)-O34[3.24] | |||||
| OD1(Asp 812)-O35[3.13] | |||||
| 2 | Enoxaparin | −7.69 | NZ(Lys 441)-O24[2.61] | MG884-O18[2.91] | Glu 350, Asp 438, Ser 507, Met 635, His 811. |
| N2-O(Asp 506)[3.10] | MG885-O18[2.88] | ||||
| OD2(Asp 537)-O18[3.01] | MG885-O25[2.47] | ||||
| NZ(Lys 631)-O30[3.12] | |||||
| NE(Arg 632)-O35[2.92] | |||||
| NH2(Arg 632)-O35[2.57] | |||||
| OG (Ser 813)-O34[3.03] | |||||
| 3 | Bemiparin | −7.96 | NZ(Lys 441)-O18[2.90] | MG884-O11[2.14] | Gly 436, Ser 539, Lys 631, Met 635. |
| NZ(Lys 441)-O8[2.93] | MG884-N1[2.51] | ||||
| O(Gln 435)-O8[2.95] | MG885-O4[2.57] | ||||
| N (Cys 540)-O13[2.91] | MG885-O1[2.99] | ||||
| OG(Ser 541)-O12[2.98] | MG885-O7[2.43] | ||||
| O(Gly 538)-O11[2.95] | |||||
| OD2(Asp 537)-N1[3.22] | |||||
| ND1(His 811)-O7[3.03] | |||||
| OD2(Asp 812)-N1[2.66] | |||||
| OD2(Asp 812)-O11[3.31] | |||||
| 4 | Fondaparinux | −12.68 | NZ(Lys 441)-O40[2.80] | MG884-O29[2.62] | Arg 423, Gln 435, Gly 436, Cys 467, Ser 507, Ser 539, Lys 631, Arg 632, Met 635, Thr 636, Ala 638, Pro 780, Asn 781, Ile 810. |
| NZ(Lys 441)-O31[2.56] | MG885-O10[2.55] | ||||
| OD2(Asp 537)-O29[2.43] | MG885-O30[2.68] | ||||
| OD2(Asp 537)-O16[3.29] | MG885-O16[2.25] | ||||
| O(Gly 538)-O29[3.22] | |||||
| OH(Tyr571)-O33[2.89] | |||||
| OD1(Asp 653)-O32[2.39] | |||||
| ND1(His 784)-O49[2.93] | |||||
| ND1(His 811)-O12[3.03] | |||||
| 5 | Idraparinux | −4.189 | NH1(Lys 423)-O39[2.72] | Nil | Gly 436, Gln 435, Asp 506, Ser 507, Arg 632, Met 635, Thr 636, Ala 638, Asp 653, Tyr 739, Ser 776, Gly 777, Pro 780, His 784, His 811. |
| NH1(Lys 425)-O4[3.06] | |||||
| NH1(Lys 425)-O42[2.87] | |||||
| NZ(Lys 441)-O23[2.88] | |||||
| NZ(Lys 441)-O48[2.70] | |||||
| NZ(Lys 631)-O31[2.84] |
Abbreviations:
a
D, donor; A, acceptor; M, Metal; X, length of interaction in Å.