AMED-BINDSのインシリコユニットでは、新型コロナウイルス(SARS-CoV-2)に対する治療法の開発を目指す研究者を支援する目的で、インシリコユニット研究者がホモロジーモデリングなどの手法で作成したSARS-CoV-2タンパク質立体構造の計算機モデルを公開します。
以下の表で“Model link”カラムがモデルファイルにリンクされています。（最終更新日: 2021年9月28日）
The insilco-unit of the AMED-BINDS releases the theoretical structural models of the SARS-CoV-2 proteins, which are constructed via methods such as homology-modeling by the researchers in this unit, in order to assist the researchers who wish to use structural models for a development of therapeutics against SARS-CoV-2.
In the following table, the items in "Model link" column are linked to the model files. (Last updated: Sep. 28, 2021)
| Gene | Protein ID | Protein name | Sequence length | Template PDB | Identity(%) | Coverage(%) | Model link | Model description | Region | Interacting protein | Ligand | Rotamer outlier(%) | Ramachandran outlier(%) | Clash score | Methods | Constructor | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | orf1ab | YP_009725297.1 | Leader protein | 180 | 2hsxA | 85.3 | 66.7 | show download |
monomer(A) | A: 10 - 129 | - | - | 0.97 | 0.0 | 4.75 | Homology modeling | JP19am0101111 |
| 2 | orf1ab | YP_009725298.1 | nsp2 | 638 | n.a. | - | - | n.d. | - | - | - | - | - | - | - | - | - |
| 3 | orf1ab | YP_009742609.1 | nsp2 | 638 | 3ld1A | - | - | show download |
- | - | - | - | - | - | - | Template-based modeling (CASP_commons) | JP19am0101110 |
| 4 | orf1ab | YP_009725299.1 | Papain-like proteinase (nsp3) | 1945 | 2idyA | 79.3 | 5.9 | show download |
monomer(A) | A: 1 - 114 | - | - | 0.98 | 0.0 | 4.55 | Homology modeling | JP19am0101111 |
| 5 | orf1ab | YP_009725299.1 | Papain-like proteinase (nsp3) | 1945 | 2favC | 72.5 | 9.2 | show download |
monomer(A) | A: 202 - 379 | - | - | 0.67 | 0.0 | 4.41 | Homology modeling | JP19am0101111 |
| 6 | orf1ab | YP_009725299.1 | Papain-like proteinase (nsp3) | 1945 | 2wctB | 76.3 | 13.9 | show download |
homo-dimer(A/B) | A/B: 410-679 | - | - | 1.27 | 0.0 | 4.96 | Homology modeling | JP19am0101111 |
| 7 | orf1ab | YP_009725299.1 | Papain-like proteinase (nsp3) | 1945 | 2kqwA | 72.7 | 3.7 | show download |
monomer(A) | A: 675 - 746 | - | - | 1.52 | 0.0 | 4.41 | Homology modeling | JP19am0101111 |
| 8 | orf1ab | YP_009725299.1 | Papain-like proteinase (nsp3) | 1945 | 5e6jA | 82.0 | 16.6 | show download |
monomer(A) | A: 745 - 1067 | - | - | 0.35 | 0.0 | 3.71 | Homology modeling | JP19am0101111 |
| 9 | orf1ab | YP_009725299.1 | Papain-like proteinase (nsp3) | 1945 | 2k87A | 81.0 | 6.3 | show download |
monomer(A) | A: 1085 - 1206 | - | - | 1.79 | 0.0 | 3.58 | Homology modeling | JP19am0101111 |
| 10 | orf1ab | YP_009725299.1 | Papain-like proteinase (nsp3) | 1945 | 4or2A,4g4sO,5uhtA | - | - | show download |
- | - | - | - | - | - | - | Template-based modeling (CASP_commons) | JP19am0101110 |
| 11 | orf1ab | YP_009725300.1 | nsp4 | 500 | 3gzfA | 40.0 | 20.4 | show download |
homo-dimer(A/B) | A: 399 - 500 B: 399 - 497 |
- | - | 1.69 | 0.0 | 3.43 | Homology modeling | JP19am0101111 |
| 12 | orf1ab | YP_009742611.1 | nsp4 | 500 | 4wa0A,6jo0A,3gzfA | - | - | show download |
- | - | - | - | - | - | - | Template-based modeling (CASP_commons) | JP19am0101110 |
| 13 | orf1ab | YP_009742611.1 | nsp4 | 500 | 2y5y | - | - | show download |
- | - | - | - | - | - | - | Template-based modeling (CASP_commons) | JP19am0101110 |
| 14 | orf1ab | YP_009725301.1 | 3C-like proteinase | 306 | 6lu7A | 100.0 | 100.0 | show download |
homo-dimer(A/C) | A/C: 1 - 306 | - | Carfilzomib | 0.0 | 0.0 | 4.54 | Homology modeling | JP19am0101111 |
| 15 | orf1ab | YP_009725302.1 | nsp6 | 290 | n.a. | - | - | n.d. | - | - | - | - | - | - | - | - | - |
| 16 | orf1ab | YP_009742613.1 | nsp6 | 290 | 3rkoC | - | - | show download |
- | - | - | - | - | - | - | Template-based modeling (CASP_commons) | JP19am0101110 |
| 17 | orf1ab | YP_009742613.1 | nsp6 | 290 | 4bwz | - | - | show download |
- | - | - | - | - | - | - | Template-based modeling (CASP_commons) | JP19am0101110 |
| 18 | orf1ab | YP_009725303.1 | nsp7 | 83 | 2kysA | 98.8 | 100.0 | show download |
monomer(A) | A: 1 - 83 | - | - | 1.3 | 0.0 | 4.57 | Homology modeling | JP19am0101111 |
| 19 | orf1ab | YP_009725304.1 | nsp8 | 198 | 2ahmH | 97.4 | 98.5 | show download |
hetero-octamer(E/F/G/H/S/T/U/V) | E/S: 35 - 195 F/T: 47 - 195 G/U: 1 - 194 H/V: 1 - 195 |
YP_009725303.1(A/B/C/D/O/P/Q/R) | - | 1.08 | 0.0 | 4.42 | Homology modeling | JP19am0101111 |
| 20 | orf1ab | YP_009725305.1 | nsp9 | 113 | 1uw7A | 97.3 | 100.0 | show download |
homo-dimer(A/B) | A/B: 1 - 113 | - | - | 1.6 | 0.0 | 4.86 | Homology modeling | JP19am0101111 |
| 21 | orf1ab | YP_009725306.1 | nsp10 | 139 | 5nfyH | 98.5 | 96.4 | show download |
hetero-dimer(B) | B: 1 - 134 | YP_009725309.1(A) | ZN | 1.23 | 0.0 | 4.78 | Homology modeling | JP19am0101111 |
| 22 | orf1ab | YP_009725307.1 | RNA-dependent RNA polymerase | 932 | 6nurA | 96.3 | 86.8 | show download |
hetero-tetramer(A) | A: 114 - 922 | YP_009725304.1(B/D), YP_009725303.1(C) | ZN | 0.81 | 0.0 | 4.87 | Homology modeling | JP19am0101111 |
| 23 | orf1ab | YP_009725308.1 | Helicase | 601 | 5wwpA | 71.5 | 99.7 | show download |
monomer(A) | A: 1 - 599 | - | ZN | 1.54 | 0.0 | 4.82 | Homology modeling | JP19am0101111 |
| 24 | orf1ab | YP_009725309.1 | 3'-to-5' Exonuclease | 527 | 5nfyD | 94.7 | 100.0 | show download |
hetero-dimer(A) | A: 1 - 527 | YP_009725306.1(B) | ZN | 1.23 | 0.0 | 4.78 | Homology modeling | JP19am0101111 |
| 25 | orf1ab | YP_009725310.1 | Endo-RNAse | 346 | 2h85A | 88.1 | 100.0 | show download |
homo-hexamer(A/B/C/D/E/F) | A/B/C/D/E/F: 1 - 346 | - | - | 0.92 | 0.0 | 4.75 | Homology modeling | JP19am0101111 |
| 26 | orf1ab | YP_009725311.1 | 2'-O-Ribose methyltransferase | 298 | 5yniA | 66.3 | 100.0 | show download |
hetero-dimer(A) | A: 1 - 298 | YP_009725306.1(B) | GTG, ZN, Sinefungin | 1.66 | 0.0 | 4.69 | Homology modeling | JP19am0101111 |
| 27 | orf1ab | YP_009725311.1 | 2'-O-Ribose methyltransferase | 298 | 5yniA | 66.3 | 100.0 | show download |
hetero-dimer(A) | A: 1 - 298 | YP_009725306.1(B) | GTG, ZN, Tecadenoson | 1.66 | 0.0 | 4.86 | Homology modeling | JP19am0101111 |
| 28 | orf1ab | YP_009725311.1 | 2'-O-Ribose methyltransferase | 298 | 5yniA | 66.3 | 100.0 | show download |
hetero-dimer(A) | A: 1 - 298 | YP_009725306.1(B) | GTG, ZN, Selodenoson | 1.66 | 0.0 | 4.55 | Homology modeling | JP19am0101111 |
| 29 | orf1ab | YP_009725311.1 | 2'-O-Ribose methyltransferase | 298 | 5yniA | 66.3 | 100.0 | show download |
hetero-dimer(A) | A: 1 - 298 | YP_009725306.1(B) | SAM, GTG, ZN, Trabodenoson | 1.66 | 0.0 | 4.4 | Homology modeling | JP19am0101111 |
| 30 | orf1ab | YP_009725312.1 | nsp11 | 13 | n.a. | - | - | n.d. | - | - | - | - | - | - | - | - | - |
| 31 | S | YP_009724390.1 | Surface glycoprotein | 1273 | 6vsbA | 100.0 | 88.6 | show download |
homo-trimer(A/B/C) | A/B/C: 13 - 1140 | ACE2(D) | EAL | 1.63 | 0.08 | 5.83 | Homology modeling | JP19am0101111 |
| 32 | S | YP_009724390.1 | Surface glycoprotein | 1273 | 6vsbA | 100.0 | 88.6 | show download |
homo-trimer(A/B/C) | A/B/C: 13 - 1140 | ACE2(D) | LPR | 1.63 | 0.08 | 5.86 | Homology modeling | JP19am0101111 |
| 33 | S | YP_009724390.1 | Surface glycoprotein | 1273 | 6vsbA | 100.0 | 88.6 | show download |
homo-trimer(A/B/C) | A/B/C: 13 - 1140 | ACE2(D) | X8Z | 1.63 | 0.08 | 5.86 | Homology modeling | JP19am0101111 |
| 34 | S | YP_009724390.1 | Surface glycoprotein | 1273 | 6vw1 | 100.0 | 88.0 | download | homo-trimer(A/B/C) | A/B/C: 27 - 1146 | - | - | - | - | - | Loop modeling | JP19am0101108 |
| 35 | ORF3a | YP_009724391.1 | ORF3a protein | 275 | 4or2A,6c0bA | - | - | show download |
- | - | - | - | - | - | - | Template-based modeling (CASP_commons) | JP19am0101110 |
| 36 | ORF3a | YP_009724391.1 | ORF3a protein | 275 | 6c0bA | - | - | show download |
- | - | - | - | - | - | - | Template-based modeling (CASP_commons) | JP19am0101110 |
| 37 | E | YP_009724392.1 | Envelope protein | 75 | 5x29E | 91.4 | 90.7 | show download |
homo-pentamer(A/B/C/D/E) | A/C/D/E: 5 - 68 B: 1 - 68 |
- | - | 1.67 | 0.0 | 4.63 | Homology modeling | JP19am0101111 |
| 38 | M | YP_009724393.1 | Membrane glycoprotein | 222 | 4hyjA,1lshA | - | - | show download |
- | - | - | - | - | - | - | Template-based modeling (CASP_commons) | JP19am0101110 |
| 39 | M | YP_009724393.1 | Membrane glycoprotein | 222 | 5xpdA | - | - | show download |
- | - | - | - | - | - | - | Template-based modeling (CASP_commons) | JP19am0101110 |
| 40 | ORF6 | YP_009724394.1 | ORF6 protein | 61 | 1cdpA | - | - | show download |
- | - | - | - | - | - | - | Template-based modeling (CASP_commons) | JP19am0101110 |
| 41 | ORF6 | YP_009724394.1 | ORF6 protein | 61 | 1lwuA | - | - | show download |
- | - | - | - | - | - | - | Template-based modeling (CASP_commons) | JP19am0101110 |
| 42 | ORF7a | YP_009724395.1 | ORF7a protein | 121 | 1yo4A | 88.4 | 75.2 | show download |
monomer(A) | A: 11 - 101 | - | - | 0.0 | 0.0 | 4.92 | Homology modeling | JP19am0101111 |
| 43 | ORF7b | YP_009725296.1 | ORF7b | 43 | 2m3eA,2mv6A,2mxbA | - | - | show download |
- | - | - | - | - | - | - | Template-based modeling (CASP_commons) | JP19am0101110 |
| 44 | ORF8 | YP_009724396.1 | ORF8 protein | 121 | 3k77A | - | - | show download |
- | - | - | - | - | - | - | Template-based modeling (CASP_commons) | JP19am0101110 |
| 45 | ORF8 | YP_009724396.1 | ORF8 protein | 121 | 3k77A | - | - | show download |
- | - | - | - | - | - | - | Template-based modeling (CASP_commons) | JP19am0101110 |
| 46 | N | YP_009724397.2 | Nucleocapsid phosphoprotein | 419 | 1sskA | 81.6 | 39.1 | show download |
monomer(A) | A: 20 - 183 | - | - | 1.56 | 0.0 | 4.88 | Homology modeling | JP19am0101111 |
| 47 | N | YP_009724397.2 | Nucleocapsid phosphoprotein | 419 | 2jw8B | 95.8 | 30.1 | show download |
homo-dimer(A/B) | A: 243 - 367 B: 242 - 367 |
- | - | 0.48 | 0.0 | 3.31 | Homology modeling | JP19am0101111 |
| 48 | ORF10 | YP_009725255.1 | ORF10 protein | 38 | 4q0yA | - | - | show download |
- | - | - | - | - | - | - | Template-based modeling (CASP_commons) | JP19am0101110 |
| 49 | orf1ab | YP_009725301.1 | 3C-like proteinase | 306 | 6lu7A | 100.0 | 100.0 | download | homo-dimer(A/C) | A/C: 1 - 306 | - | Cepharanthine | 0.0 | 0.0 | 4.54 | Homology modeling | JP19am0101111 |
| 50 | S | YP_009724390.1 | Surface glycoprotein | 1273 | 6m0jE | 100.0 | 15.3 | download | monomer(A) | A:333-527 | ACE2(D) | Cepharanthine | - | - | - | - | JP19am0101111 |
| 51 | NPC1 | NP_000262.2 | Niemann-Pick type C intracellular cholesterol transporter 1 | 1278 | 6w5v, 6nq0 | 100.0 | 96.5 | download | hetero-dimer(A) | A: 23 - 1255 | NPC2(T) | Cepharanthine | - | - | - | - | JP19am0101111 |
| 52 | TPCN2 | NP_620714.2 | Two pore calcium channel protein 2 | 752 | 6nq0 | 100.0 | 88.2 | download | homo-dimer(A/B) | A: 39 - 701 | - | Cepharanthine | - | - | - | - | JP19am0101111 |