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新型コロナウイルスの構造情報

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コロナウイルス
コロナウイルス, 2020. David S. Goodsell@RCSB PDB による原画を修正

最近、新型コロナウイルス感染症(Novel Coronavirus disease 2019: COVID-19)の拡大が世界中で深刻な問題となっています。早急にこの新型ウイルス(Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2)を理解し有効な薬を開発するため,関連するタンパク質の構造研究は既に始まっています。そして,解明された構造はPDBに登録されていっています。PDBjでは利用者の利便を図るため,新型コロナウイルス特集ページを作成しました。新たなエントリーが毎週水曜日の週次更新で公開されると、同時にこのページにも追加されます。

またこのウイルスのタンパク質に関する解説記事を以下の「今月の分子」ページに掲載しています。

「全エントリー」のタブでは,同じ著者によるグループ登録のエントリーも全て区別し,すべてのPDB IDを省略せず表示しています。 「代表構造」タブには最も分解能の高い代表構造のみを表示しており,アミノ酸配列が100%同じPDBエントリーはリガンドが異なるものも含め除外してあります。 「最新のエントリー」のタブは,今週公開された最も新しいエントリーです。


作成日: 2020-09-03 (最終更新日: more than 1 year ago)2022-09-02
7Z85
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CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-B5 nanobody complex
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanobody H11-B5, ...
著者Weckener, M, Naismith, J.H.
登録日2022-03-16
公開日2022-07-13
最終更新日2022-10-05
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.
Proc.Natl.Acad.Sci.USA, 119, 2022
7Z86
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CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-H4 Q98R H100E nanobody complex in 1Up2Down conformation
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanobody H11-H4 Q98R H100E, ...
著者Weckener, M, Naismith, J.H.
登録日2022-03-16
公開日2022-07-13
最終更新日2022-10-05
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.
Proc.Natl.Acad.Sci.USA, 119, 2022
7Z9Q
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CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-A10 nanobody complex
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanobody H11-A10, ...
著者Weckener, M, Naismith, J.H.
登録日2022-03-21
公開日2022-07-13
最終更新日2022-10-05
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.
Proc.Natl.Acad.Sci.USA, 119, 2022
7Z9R
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CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-H4 Q98R H100E nanobody complex in 2Up1Down conformation
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanobody H11-H4 Q98R H100E, ...
著者Weckener, M, Naismith, J.H.
登録日2022-03-21
公開日2022-07-13
最終更新日2022-10-05
実験手法ELECTRON MICROSCOPY (4.2 Å)
主引用文献Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.
Proc.Natl.Acad.Sci.USA, 119, 2022
8D4J
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BU of 8d4j by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) H172Y Mutant
分子名称: 3C-like proteinase nsp5, GLYCEROL
著者Lewandowski, E.M, Hu, Y, Tan, H, Wang, J, Chen, Y.
登録日2022-06-02
公開日2022-07-13
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.78 Å)
主引用文献Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir.
Biorxiv, 2022
8D4K
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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) H172Y Mutant in Complex with Inhibitor GC376
分子名称: (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase nsp5
著者Lewandowski, E.M, Hu, Y, Tan, H, Wang, J, Chen, Y.
登録日2022-06-02
公開日2022-07-13
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.89 Å)
主引用文献Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir.
Biorxiv, 2022
8D4L
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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) S144A Mutant
分子名称: 3C-like proteinase nsp5
著者Lewandowski, E.M, Hu, Y, Tan, H, Wang, J, Chen, Y.
登録日2022-06-02
公開日2022-07-13
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir.
Biorxiv, 2022
8D4M
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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) S144A Mutant in Complex with Inhibitor GC376
分子名称: (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase nsp5
著者Lewandowski, E.M, Hu, Y, Tan, H, Wang, J, Chen, Y.
登録日2022-06-02
公開日2022-07-13
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.81 Å)
主引用文献Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir.
Biorxiv, 2022
8D4N
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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) E166Q Mutant
分子名称: 3C-like proteinase nsp5
著者Lewandowski, E.M, Hu, Y, Tan, H, Wang, J, Chen, Y.
登録日2022-06-02
公開日2022-07-13
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir.
Biorxiv, 2022
8DCZ
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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir
分子名称: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
著者Lewandowski, E.M, Hu, Y, Tan, H, Wang, J, Chen, Y.
登録日2022-06-17
公開日2022-07-13
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.38 Å)
主引用文献Naturally Occurring Mutations of SARS-CoV-2 Main Protease Confer Drug Resistance to Nirmatrelvir.
Acs Cent.Sci., 9, 2023
8DD1
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SARS-CoV-2 Main Protease (Mpro) H164N Mutant in Complex with Inhibitor GC376
分子名称: (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase nsp5
著者Lewandowski, E.M, Butler, S.G, Hu, Y, Tan, H, Wang, J, Chen, Y.
登録日2022-06-17
公開日2022-07-13
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.03 Å)
主引用文献Naturally Occurring Mutations of SARS-CoV-2 Main Protease Confer Drug Resistance to Nirmatrelvir.
Acs Cent.Sci., 9, 2023
8DD9
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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) S144L Mutant in Complex with Inhibitor GC376
分子名称: (1R,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase nsp5
著者Lewandowski, E.M, Jacobs, L.M.C, Hu, Y, Tan, H, Wang, J, Chen, Y.
登録日2022-06-17
公開日2022-07-13
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.04 Å)
主引用文献Naturally Occurring Mutations of SARS-CoV-2 Main Protease Confer Drug Resistance to Nirmatrelvir.
Acs Cent.Sci., 9, 2023
8DFE
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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) S144L Mutant
分子名称: 3C-like proteinase nsp5
著者Lewandowski, E.M, Jacobs, L.M.C, Hu, Y, Tan, H, Wang, J, Chen, Y.
登録日2022-06-22
公開日2022-07-13
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (1.89 Å)
主引用文献Naturally Occurring Mutations of SARS-CoV-2 Main Protease Confer Drug Resistance to Nirmatrelvir.
Acs Cent.Sci., 9, 2023
8DFN
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BU of 8dfn by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) H164N Mutant
分子名称: 3C-like proteinase nsp5
著者Lewandowski, E.M, Butler, S.G, Hu, Y, Tan, H, Wang, J, Chen, Y.
登録日2022-06-22
公開日2022-07-13
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.04 Å)
主引用文献Naturally Occurring Mutations of SARS-CoV-2 Main Protease Confer Drug Resistance to Nirmatrelvir.
Acs Cent.Sci., 9, 2023
8DGB
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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Q192T Mutant in Complex with Inhibitor GC376
分子名称: (1R,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase nsp5
著者Lewandowski, E.M, Jacobs, L.M.C, Hu, Y, Tan, H, Wang, J, Chen, Y.
登録日2022-06-23
公開日2022-07-13
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.87 Å)
主引用文献Naturally Occurring Mutations of SARS-CoV-2 Main Protease Confer Drug Resistance to Nirmatrelvir.
Acs Cent.Sci., 9, 2023
7EN8
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Crystal structure of SARS-CoV-2 3CLpro in complex with the non-covalent inhibitor WU-04
分子名称: 3C-like proteinase, GLYCEROL, ~{N}-[(1~{S},2~{R})-2-[[4-bromanyl-2-(methylcarbamoyl)-6-nitro-phenyl]amino]cyclohexyl]isoquinoline-4-carboxamide
著者Hou, N, Peng, C, Hu, Q.
登録日2021-04-16
公開日2022-07-20
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.83 Å)
主引用文献Development of Highly Potent Noncovalent Inhibitors of SARS-CoV-2 3CLpro.
Acs Cent.Sci., 9, 2023
7EN9
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Crystal structure of SARS-CoV-2 3CLpro in complex with the non-covalent inhibitor WU-02
分子名称: 3C-like proteinase, 5-bromanyl-~{N}-methyl-3-nitro-2-[(4~{R},5~{S})-2-(7-oxidanylisoquinolin-4-yl)carbonyl-4-phenyl-2,7-diazaspiro[4.4]nonan-7-yl]benzamide
著者Hou, N, Peng, C, Hu, Q.
登録日2021-04-16
公開日2022-07-20
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Development of Highly Potent Noncovalent Inhibitors of SARS-CoV-2 3CLpro.
Acs Cent.Sci., 9, 2023
7P2O
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NMR solution structure of SUD-C domain of SARS-CoV-2
分子名称: Non-structural protein 3
著者Gallo, A, Tsika, A.C, Fourkiotis, N.K, Spyroulias, G.A.
登録日2021-07-06
公開日2022-07-20
最終更新日2024-06-19
実験手法SOLUTION NMR
主引用文献NMR solution structure of SUD-C domain of SARS-CoV-2
To Be Published
7RVM
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Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI11
分子名称: 3C-like proteinase, N-[(benzyloxy)carbonyl]-L-valyl-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-methyl-L-leucinamide
著者Yang, K, Liu, W.
登録日2021-08-19
公開日2022-07-20
最終更新日2024-04-03
実験手法X-RAY DIFFRACTION (1.95 Å)
主引用文献A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals.
Eur.J.Med.Chem., 240, 2022
7RVN
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Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI12
分子名称: 3C-like proteinase, DIMETHYL SULFOXIDE, N-[(benzyloxy)carbonyl]-L-valyl-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-methylidene-L-norvalinamide
著者Yang, K, Liu, W.
登録日2021-08-19
公開日2022-07-20
最終更新日2023-11-15
実験手法X-RAY DIFFRACTION (1.63 Å)
主引用文献A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals.
Eur.J.Med.Chem., 240, 2022
7RVO
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Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI13
分子名称: 3C-like proteinase, N-[(benzyloxy)carbonyl]-L-valyl-3-cyclopropyl-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-alaninamide
著者Yang, K, Sankaran, B, Liu, W.
登録日2021-08-19
公開日2022-07-20
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals.
Eur.J.Med.Chem., 240, 2022
7RVP
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Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI14
分子名称: 3C-like proteinase, N-[(benzyloxy)carbonyl]-L-valyl-3-furan-2-yl-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-alaninamide
著者Yang, K, Sankaran, B, Liu, W.
登録日2021-08-19
公開日2022-07-20
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals.
Eur.J.Med.Chem., 240, 2022
7RVQ
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Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI16
分子名称: 3C-like proteinase, N-[(benzyloxy)carbonyl]-O-tert-butyl-L-threonyl-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-methyl-L-leucinamide
著者Yang, K, Liu, W.
登録日2021-08-19
公開日2022-07-20
最終更新日2023-11-15
実験手法X-RAY DIFFRACTION (2.48 Å)
主引用文献A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals.
Eur.J.Med.Chem., 240, 2022
7RVR
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Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI18
分子名称: 3C-like proteinase, N-[(benzyloxy)carbonyl]-3-methyl-L-valyl-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-methyl-L-leucinamide
著者Yang, K, Liu, W.
登録日2021-08-19
公開日2022-07-20
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.46 Å)
主引用文献A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals.
Eur.J.Med.Chem., 240, 2022
7RVS
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Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI19
分子名称: 3C-like proteinase, N-[(benzyloxy)carbonyl]-3-methyl-L-valyl-3-cyclopropyl-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-alaninamide
著者Yang, K, Liu, W.
登録日2021-08-19
公開日2022-07-20
最終更新日2023-11-15
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals.
Eur.J.Med.Chem., 240, 2022

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