Table 2.
Results of Docking of S Protein, ACE-2, and rfhSP-D
| S. Number | Receptor | Ligand | Binding Energy (kcal/mol) | Interactions |
|
|---|---|---|---|---|---|
| Receptor* | Ligand† | ||||
| 1 | ACE-2 | S Protein | Crystal structure | Ser19 | Ala475 |
| Gln24 | Asn487 | ||||
| Lys31 | Phe456, Glu484, Tyr489, Gln493 | ||||
| His34 | Leu455, Tyr453 | ||||
| Glu35 | Gln493 | ||||
| Glu37 | Tyr505 | ||||
| Asp38 | Tyr449 | ||||
| Tyr41 | Thr500 | ||||
| Gln42 | Gln498 | ||||
| Met82 | Phe486‡ | ||||
| Tyr83 | Gly496, Asn487, Tyr489 | ||||
| Glu329 | Arg439 | ||||
| Lys353 | Tyr505, Gly502 | ||||
| Gly354 | Tyr505 | ||||
| 2 | rfhSP-D | S protein (open) | −20.63 | Gln219 | Gln493 |
| His220 | Tyr449 | ||||
| Ala223 | Gln493, Phe490 | ||||
| Ser226 | Ser494 | ||||
| Lys229 | Tyr449 | ||||
| Ser239 | Asn450 | ||||
| Gly241 | Asn448, Gln498 | ||||
| Glu242 | Gln498 | ||||
| Gln263 | Arg346 | ||||
| Thr308 | Arg466 | ||||
| 3 | ACE-2 | rfhSP-D | −24.30 | Ser19 | Ser328 |
| Asp30 | Thr255 | ||||
| Lys31 | Thr305 | ||||
| His34 | Gln258 | ||||
| Glu35 | Pro307, Gly309 | ||||
| Glu75 | Lys299 | ||||
| Gly319 | Ala275 | ||||
| Pro321 | Ala275 | ||||
| Gln552 | Ala274, Tyr314 | ||||
Definition of abbreviations: ACE-2 = angiotensin-converting enzyme 2; rfhSP-D = recombinant fragment of human SP-D; S protein = Spike protein.
*
The ACE2 residues in bold typeface interact with both S protein and rfhSP-D (docked structure).
†
The S protein residues in bold are predicted to be part of the common binding site for ACE-2 and rfhSP-D.
‡
The structural coordinates of Phe486 are missing in the open conformation S protein (Protein Data Bank identification 6VYB).