Table 1.
Information of the D3Targets-2019-nCoV database.
| No. | Target full name | Target abbreviation | Protein ID/UniProtKB | State/conformation | Marka | Number of pocketsb | Orthosteric pocketsc | PDB ID | Sequence similarity (%) |
|---|---|---|---|---|---|---|---|---|---|
| 1 | Host translation inhibitor nsp 1 | Nsp 1 | QHD43415.1 | /d | V1 | 3 | / | 2HSX | 86.09 |
| 2 | Non-structural protein 2 | Nsp 2 | QHD43415.1 | / | V2 | 13 | / | / | / |
| 3 | Papain-like proteinase | PLP/PLpro | QHD43415.1 | Monomer | V3-1 | 6 | 1 | 3E9S | 82.86 |
| Dimer | V3-2 | 9 | 1 | 5Y3E | 82.80 | ||||
| 4 | ADP ribose phosphatase | ADRP | QHD43415.1 | Monomer | V4-1* | 1 | 1 | 6W02 | / |
| Dimer | V4-2* | 5 | 2, 3 | 6W02 | / | ||||
| 5 | Non-structural protein 4 | Nsp 4 | QHD43415.1 | / | V5 | 7 | / | / | / |
| 6 | 3C-like proteinase | 3CLpro/Mpro | QHD43415.1 | Monomer | V6-1 | 4 | 2 | 1Z1I | 96.01 |
| Monomer | V6-2* | 7 | 1 | 5R82 | / | ||||
| Dimer | V6-3 | 6 | 3, 4 | 2Z9J | 96.08 | ||||
| Dimer | V6-4* | 7 | 3, 4 | 6Y2G | / | ||||
| MD1# | V6-5 | 6 | 1 | 1Z1I | 96.01 | ||||
| MD2# | V6-6 | 6 | 2 | 1Z1I | 96.01 | ||||
| MD3# | V6-7 | 6 | 3 | 1Z1I | 96.01 | ||||
| MD4# | V6-8 | 7 | 3 | 1Z1I | 96.01 | ||||
| 7 | Non-structural protein 6 | Nsp 6 | QHD43415.1 | / | V7 | 7 | / | / | / |
| 8 | Non-structural protein 7 | Nsp 7 | QHD43415.1 | / | V8 | 1 | / | 1YSY | 98.80 |
| 9 | Non-structural protein 8 | Nsp 8 | QHD43415.1 | / | V9 | 1 | / | 2AHM | 97.42 |
| 10 | Non-structural protein 9 | Nsp 9 | QHD43415.1 | Monomer | V10-1 | 3 | / | 1UW7 | 97.35 |
| Monomer | V10-2* | 3 | / | 6W4B | / | ||||
| Dimer | V10-3 | 7 | / | 1QZ8 | 97.35 | ||||
| Dimer | V10-4* | 6 | / | 6W4B | / | ||||
| 11 | Non-structural protein 10 | Nsp 10 | QHD43415.1 | / | V11 | 3 | / | 5NFY | 98.47 |
| 12 | RNA-dependent RNA polymerase | RdRp | QHD43415.1 | / | V12-1 | 10 | / | 6NUR | 96.35 |
| +Mg2+ | V12-2 | 10 | / | 6NUR | 96.35 | ||||
| 13 | Helicase | / | QHD43415.1 | Monomer | V13-1 | 11 | / | 6JYT | 99.83 |
| Dimer | V13-2 | 21 | / | 6JYT | 99.83 | ||||
| 14 | Guanine-N7 methyltransferase | N7 Mtase | QHD43415.1 | / | V14 | 12 | 1 | 5NFY | 94.88 |
| 15 | Uridylate-specific endoribonuclease | NendoU | QHD43415.1 | Monomer | V15-1 | 7 | / | 2H85 | 88.12 |
| Monomer | V15-2* | 8 | / | 6W01 | / | ||||
| Dimer | V15-3* | 15 | / | 6W01 | / | ||||
| 16 | 2ʹ-O-Methyltransferase | 2ʹ-O-Mtase | QHD43415.1 | / | V16 | 5 | 1 | 2XYR | 93.49 |
| 17 | ORF7a protein | / | QHD43421.1 | / | V17 | 1 | / | 1YO4 | 91.57 |
| 18 | Spike protein | S protein | QHD43416.1 | Closed | V18-1 | 25 | / | 5X58 | 76.48 |
| Closed | V18-2* | 30 | / | 6VXX | / | ||||
| Open | V18-3 | 27 | / | 5 × 5B | 76.48 | ||||
| Open | V18-4* | 42 | / | 6VYB | / | ||||
| Heptad repeat 1 | V18-5 | 12 | / | 5ZVM | 87.50 | ||||
| S2 subunit | V18-6* | 4 | 6LXT | / | |||||
| 19 | Envelope protein | E protein | QHD43418.1 | Monomer | V19-1 | 1 | / | 2MM4 | 91.38 |
| Pentamer | V19-2 | 2 | / | 5X29 | 91.38 | ||||
| 20 | Nucleocapsid phosphoprotein | N protein | QHD43423.2 | C terminal | V20-1 | 1 | / | 2GIB | 96.04 |
| N terminal monomer | V20-2 | 4 | / | 2OFZ | 92.06 | ||||
| N terminal monomer | V20-3* | 3 | / | 6VYO | / | ||||
| N terminal-tetramer | V20-4* | 16 | / | 6VYO | / | ||||
| 21 | Angiotensin converting enzyme 2 | ACE2 | P59594 | / | H1* | 6 | / | 1R42 | / |
| 22 | Cathepsin L | CTSL | P07711 | / | H2* | 5 | 1 | 2XU3 | / |
| 23 | Transmembrane protease serine 2 | TMPRSS2 | O15393 | / | H3 | 10 | / | / | / |
| 24 | C type lectin domain family four member M | CLEC4M | Q9H2X3 | / | H4* | 2 | / | 1XAR | / |
| 25 | AP2-associated protein kinase 1 | AAK1 | Q2M2I8 | / | H5* | 12 | 1, 6 | 5TE0 | / |
| 26 | Cyclophilin A | CypA | P62937 | / | H6* | 3 | 1 | 4N1M | / |
| 27 | Disintegrin and metalloproteinase domain-containing protein 17 | ADAM17 | P78536 | / | H7-1 | 5 | 1 | 2I47 | 99.21 |
| +Zn2+ | H7-2 | 5 | 1 | 2I47 | 99.21 | ||||
| 28 | Furin | / | P09958 | / | H8* | 8 | 1 | 5JXG | / |
| 29 | Tyrosine-protein kinase ABL2 | ABL2 | P42684 | / | H9* | 3 | 1 | 3HMI | / |
| 30 | Eukaryotic initiation factor 4A-I | eIF4A | P60842 | / | H10* | 8 | 2 | 5ZC9 | / |
| 31 | Dihydroorotate dehydrogenase | DHODH | Q02127 | / | H11* | 6 | 1 | 3U2O | / |
| 32 | Glycogen synthase kinase-3 beta | GSK3β | P49841 | / | H12* | 13 | 1 | 1J1B | / |
| 33 | Heterogeneous nuclear ribonucleoprotein A1 | HNRNPA1 | P09651 | / | H13* | 4 | / | 1U1Q | / |
| 34 | Calnexin | / | P27823 | / | H14-1 | 7 | / | 1JHN | 95.73 |
| +Ca2+ | H14-2 | 7 | / | 1JHN | 95.73 | ||||
| 35 | Mitogen-activated protein kinase 8 | JNK1 | P45983 | / | H15 | 12 | 1 | 2G01 | 99.44 |
| 36 | Mitogen-activated protein kinase 9 | JNK2 | P45984 | / | H16 | 6 | 1 | 3NPC | 98.31 |
| 37 | Mitogen-activated protein kinase 10 | JNK3 | P53779 | / | H17* | 7 | 1 | 1JNK | / |
| 38 | RAC-alpha serine/threonine-protein kinase | AKT1 | P31749 | / | H18* | 8 | 1 | 3O96 | / |
| 39 | RAC-beta serine/threonine-protein kinase | AKT2 | P31751 | / | H19* | 12 | 1 | 3D0E | / |
| 40 | RAC-gamma serine/threonine-protein kinase | AKT3 | Q9Y243 | / | H20* | 5 | / | 2X18 | / |
| 41 | Caveolin-2 | CAV2 | P51636 | / | H21 | 2 | / | / | / |
| 42 | cGMP-specific 3ʹ,5ʹ-cyclic phosphodiesterase | PDE5 | O76074 | / | H22* | 10 | 1 | 2H44 | / |
*Crystal structures of SARS-CoV-2 or human proteins downloaded from PDB.
#Conformations clustered from molecular dynamics trajectories.
a
V refers to the SARS-CoV-2 protein, and H refers to the human protein.
b
The number of predicted binding pockets by D3Pockets on the protein with the PPV greater than 200 Å3.
c
The orthosteric ligand binding sites assigned based on its sequence similarity (>80%) to that of its homologous proteins.
d
Not available.