Table 1.
Characterization of the binding pockets identified on the X-ray structure and on the 8 representative structures obtained from the cluster analysis in terms of SASA (solvent accessible surface area), volume and main interacting amino acid residues at the angiotensin-converting enzyme 2 (ACE2) and S1 RBD interface. Values obtained with FPocket.
| Cluster | Total SASA (Å2) | Polar SASA (Å2) | Non-Polar SASA (Å2) | Volume (Å3) | ACE2 Main Residues | S1 RDB Main Residues | |
|---|---|---|---|---|---|---|---|
| X-ray | 1 | 141.0 | 75.8 | 65.2 | 351.1 | Asn33, His34, Glu37, Lys353 | Arg403, Lys417, Tyr453, Tyr495, Tyr505, |
| 2 | 193.8 | 98.4 | 95.4 | 738.9 | Gln42, Leu45, Asn49, Asn61, Asn64, Lys68 | Gly446, Tyr449 | |
| 3 | 241.4 | 115.8 | 125.6 | 827.5 | Thr324, Phe356, Arg393 | Gly502, Val503, Tyr505 | |
| Cluster 1 | 1 | 223.5 | 134.1 | 89.4 | 828.7 | Asn33, His34, Glu37, Asp38, Lys353, Pro389, Phe390 | Arg403, Glu406, Lys417, Ile418, Tyr495, Tyr505 |
| 2 | 155.7 | 79.6 | 76.1 | 543.4 | Phe28, Lys31, Phe32, Glu35, Asp38, Leu39, Phe72, Gln76, Leu79 | Glu484, Phe486, Asn487, Tyr489 | |
| 3 | 152.0 | 43.3 | 108.7 | 525.8 | Thr324, Gln325, Asn330, Asp355, Phe356 | Val503, Tyr505 | |
| Cluster 2 | 1 | 304.7 | 173.1 | 131.6 | 919.7 | His34, Glu37, Asp38, Lys353, Pro389, Arg393 | Arg403, Gln409, Lys417, Ile418, Tyr495 |
| 2 | 174.4 | 112.2 | 62.2 | 549.8 | Lys31, Gln76, Leu79 | Glu484, Tyr489, Phe490 | |
| Cluster 3 | 1 | 207.3 | 98.6 | 108.7 | 603.1 | Lys353, Phe356, Arg393 | Asp405, Tyr505 |
| 2 | 257.4 | 142.6 | 114.7 | 750.6 | Thr324, Gln325, Glu329, Asp355 | Thr500, Gly502, Val503 | |
| Cluster 4 | 1 | 213.1 | 128.6 | 84.5 | 642.8 | Asn33, His34, Pro389, Arg393 | Arg403, Asp405, Lys417 |
| Cluster 5 | 1 | 232.1 | 122.2 | 109.9 | 784.6 | Asn33, His34, Pro389, Phe390 | Asp405, Lys417, Ile418, Tyr495, Tyr505 |
| Cluster 6 | 1 | 155.8 | 96.6 | 59.2 | 535.4 | Asp30, Asn33, His34, Glu37, Asp38, Lys353, Phe390 | Arg403, Lys417, Tyr495, Tyr505 |
| 2 | 187.7 | 75.4 | 112.3 | 566.0 | Asp350, Phe356, Tyr385, Arg393 | Gly502, Tyr505 | |
| Cluster 7 | 1 | 175.3 | 107.7 | 67.6 | 565.9 | Glu37, Asp38, Leu39, Lys353 | Leu452, Arg403, Gln493, Tyr495, Tyr505 |
| 1 | 285.5 | 128.5 | 157.0 | 833.7 | Asn33, Thr324, Gln325, Phe356, Pro389, Arg393 | Arg403, Asp405, Val503 | |
| Cluster 8 | 1 | 252.0 | 144.5 | 107.5 | 799.2 | Thr20, Glu23, Gln24, Lys26, Thr27, Asp30 | Lys417, Tyr421, Phe456, Tyr473, Ala475 |