Table 1.
Identification and cross validation of potential allosteric sites on SARS-CoV-2 prefusion S-protein using multiple predictive algorithms.
| Predicted sites | Binding site prediction and cross-validation |
Corresponding S-protein domain | |||
|---|---|---|---|---|---|
| SiteMap | Fpocket | DS 2016 Client | Prankweb | ||
| Site 1 | 65, 66, 95–115, 121–136, 202, 201, 203, 204, 205, 206, 211, 221, 222, 223 | 101, 103, 104, 108, 109, 142, 143, 144, 145, 146, 147, 178 | 92,93, 94, 95,96, 97, 98, 99, 101, 102, 103, 104, 105, 106, 117–129, 170–175, 189–194, 203–207, 223, 224, 225 | 99, 101, 102, 104, 119, 120, 121, 126, 172, 173, 175, 177, 190, 192, 203, 205 | NTD |
| Site 2 | 731-737, 791–806, 815,819, 823–828, 833–840, 951, 954, 959, 962-968 | 705-713, 720, 789, 792, 793, 794, 807, 832, 833, 834, 835, 836, 837, 840, 848, 852–863, 904, 908–910, 947-960 | 726, 727, 822–837, 845–854, 856–861, 944-963 | 828, 833, 837, 854, 856, 858, 859, 860, 956, 959, 960, 963 | FP, HR1, CD |
| Site 3 | 18, 19, 20, 21, 22, 23, 53–61, 288–293, 585–593, 623-635 | 13, 28, 47, 50, 51, 53, 54, 57, 317, 318, 372 | 37, 38, 39, 40, 41, 42, 51, 52,53, 54, 55, 195-204 | 50, 51, 52, 273, 274, 291, 292, 298, 301, 302, 304, 315, 317, 631, 632 | NTD, RBD, SD1 |
| Site 4 | 363, 364, 365, 366, 367, 368, 369, 370, 382, 383, 385, 423–434, 512, 513, 514, 515 | 355, 380, 396, 398, 412, 423, 425, 426, 429, 430, 431, 432, 433, 464, 512, 513, 514, 515, 516, 518 | 326, 327, 328, 329, 330, 331, 357, 358, 359, 360, 361, 362, 363, 380–396, 428, 429, 430, 431, 432, 513–526, 541–548, 559-580 | 355-360, 396, 398, 425, 426, 429, 430, 431, 433, 464, 466, 514, 515, 516 | RBD, SD1 |
| Site 5 | 596-603, 660–674, 697–702, 710,711, 712, 713, 714, 715, 716, 717, 718, 719, 775-781 | 769, 774, 797, 798, 800, 882, 883, 895, 896, 897, 898, 899, 902, 916, 920, 923 | 719-734, 769–785, 833, 860–875, 1069 | 729, 730, 731, 774, 775, 778, 782, 830, 863, 865, 867, 870, 1056, 1058, 1059 | SD1, CR, HR1 |
| Site 6 | 1068, 1069, 1077, 1078, 1079, 1080, 1089, 1090, 1091, 1092, 1093, 1094, 1095, 1105, 1106, 1107 | 1010, 1012, 1015, 1019, 1108, 1119, 1208, 1210, 1211, 1212, 1214, 1215, 1218 | 909. 910, 911, 1089, 1090, 1091, 1092, 1093, 1094, 1104, 1105, 1106, 1107, 1108, 1109, 1207-1216 | 1081, 1083, 1084, 1088, 1115, 1116, 1117, 1122, 1123, 1136, 1137, 1138, 1201 | SD2, βH, TM, CH |
NTD, N-terminal domain; FP, fusion peptide; HR1, heptad repeat 1; CD, connector domain; RBD, receptor binding domain; SD2, subdomain 2; SD1, subdomain 1; CH, central helix; βH – β hairpin; TM, transmembrane region.