Table 1.
The structural description of eleven probable drug targets (with known 3D structures) that are involved in the virulence and pathogenesis of SARS-CoV-2.
| PDB ID | Name of the protein | Chain | Resolution | R-Value Free | R-Value Work | Experimental method | Secondary structure | References |
|---|---|---|---|---|---|---|---|---|
| 1WYY | Post-fusion hairpin conformation of the spike glycoprotein | A, B | 2.2 Å | 0.249 | 0.210 | X-ray diffraction | 66% helical | Duquerroy et al., 2005 |
| 6VYB | SARS-CoV-2 spike ectodomain structure (open state) | A, B, C | 3.2 Å | Aggregation state: Particle | Reconstruction method: Single particle | Electron Microscopy | 16% helical, 25% beta sheet | Walls et al., 2020 |
| 6VXX | Structure of the SARS-CoV-2 spike glycoprotein (closed state) | A, B, C | 2.8 Å | Aggregation state: Particle | Reconstruction method: Single particle | Electron Microscopy | 16% helical, 25% beta sheet | Walls et al., 2020 |
| 1Q2W | X-Ray Crystal Structure of the SARS Coronavirus Main Protease | A, B | 1.86 Å | 0.249 | 0.194 | X-ray diffraction | 24% helical, 28% beta sheet | Bonanno et al., 2003 |
| 5RE4 | Crystal Structure of SARS-CoV-2 main protease in complex with Z1129283193 | A | 1.88 Å | 0.266 | 0.199 | X-ray diffraction | 26% helical, 28% beta sheet | Fearon et al., to be published |
| 3I6G | Newly identified epitope Mn2 from SARS-CoV M protein complexed withHLA-A*0201 | C, F | 2.201 Å | 0.246 | 0.205 | X-ray diffraction | 26% helical, 39% beta sheet | Liu et al., 2010 |
| 2MM4 | Structure of a Conserved Golgi Complex-targeting Signal in Coronavirus Envelope Proteins | A | – | Conformers Calculated: 200 | Conformers Submitted: 15 | NMR | 65% helical | Li et al., 2014 |
| 1XAK | Structure of the sars-coronavirus orf7a accessory protein | A | 1.8 Å | 0.275 | 0.223 | X-ray diffraction | 48% beta sheet | Nelson et al., 2005 |
| 2CME | The crystal structure of SARS coronavirus ORF-9b protein | A | 2.8 Å | 0.289 | 0.266 | X-ray diffraction | 3% helical, 44% beta sheet | Meier et al., 2006 |
| 6M17 | The 2019-nCoV RBD/ACE2-B0AT1 complex | E, F | 2.9 Å | Aggregation state: Particle | Reconstruction method: Single particle | Electron Microscopy | 3% helical, 23% beta sheet | Yan et al., 2020 |
| 6M71 | SARS-Cov-2 RNA-dependent RNA polymerase in complex with cofactors | A, B. C, D | 2.9 Å | Aggregation state: Particle | Reconstruction method: Single particle | Electron Microscopy | 47% helical, 17% beta sheet | Gao et al., 2020 |