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: 2020年4月13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: Apr. 13, 2020)

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
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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
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- - - - - - - Template-based modeling (CASP_commons) JP19am0101110
4 orf1ab YP_009725299.1 Papain-like proteinase (nsp3) 1945 2idyA 79.3 5.9 show
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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
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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
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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
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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
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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
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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
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- - - - - - - Template-based modeling (CASP_commons) JP19am0101110
11 orf1ab YP_009725300.1 nsp4 500 3gzfA 40.0 20.4 show
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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
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- - - - - - - Template-based modeling (CASP_commons) JP19am0101110
13 orf1ab YP_009742611.1 nsp4 500 2y5y - - show
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- - - - - - - Template-based modeling (CASP_commons) JP19am0101110
14 orf1ab YP_009725301.1 3C-like proteinase 306 6lu7A 100.0 100.0 show
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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
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- - - - - - - Template-based modeling (CASP_commons) JP19am0101110
17 orf1ab YP_009742613.1 nsp6 290 4bwz - - show
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- - - - - - - Template-based modeling (CASP_commons) JP19am0101110
18 orf1ab YP_009725303.1 nsp7 83 2kysA 98.8 100.0 show
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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- - - - - - - Template-based modeling (CASP_commons) JP19am0101110
36 ORF3a YP_009724391.1 ORF3a protein 275 6c0bA - - show
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- - - - - - - Template-based modeling (CASP_commons) JP19am0101110
37 E YP_009724392.1 Envelope protein 75 5x29E 91.4 90.7 show
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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
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- - - - - - - Template-based modeling (CASP_commons) JP19am0101110
39 M YP_009724393.1 Membrane glycoprotein 222 5xpdA - - show
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- - - - - - - Template-based modeling (CASP_commons) JP19am0101110
40 ORF6 YP_009724394.1 ORF6 protein 61 1cdpA - - show
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- - - - - - - Template-based modeling (CASP_commons) JP19am0101110
41 ORF6 YP_009724394.1 ORF6 protein 61 1lwuA - - show
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- - - - - - - Template-based modeling (CASP_commons) JP19am0101110
42 ORF7a YP_009724395.1 ORF7a protein 121 1yo4A 88.4 75.2 show
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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
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- - - - - - - Template-based modeling (CASP_commons) JP19am0101110
44 ORF8 YP_009724396.1 ORF8 protein 121 3k77A - - show
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- - - - - - - Template-based modeling (CASP_commons) JP19am0101110
45 ORF8 YP_009724396.1 ORF8 protein 121 3k77A - - show
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- - - - - - - Template-based modeling (CASP_commons) JP19am0101110
46 N YP_009724397.2 Nucleocapsid phosphoprotein 419 1sskA 81.6 39.1 show
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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
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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
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- - - - - - - Template-based modeling (CASP_commons) JP19am0101110